Jay Cooke

Your landlord is not allowed to charge VAT on residential rent, regardless of what the property was previously. Ask your landlord for a VAT receipt/VAT invoice, that will at least check to see if landlord is VAT registered, if landlord refuses to issue a VAT invoice (which is also a legal requirement), then you probably have a landlord pocketing the 20% and not handing it over to HMRC. However, this is a legal matter between you and the landlord, what does your lease/rental agreement say about VAT?

On what basis would you reclaim ALL the VAT (100%) when you clearly know that you are making exempt supplies already? If you did not have any exempt income and had not developed your business plan, then there could be an argument that as your intention is not known you reclaim all of the input tax initially and then repay a proportion back, but as you do know you are making exempt supplies then to argue you are entitled to 100% of VAT recovery makes little sense. Even if you do choose to reclaim 100% of the VAT, you are aware that there is an annual adjustment which must be performed and may see previously reclaimed input tax paid back to HMRC. If the cost of the refurbishment is over £250k net then you will also need to perform Capital Goods Scheme (CGS) calculations, each year for 10 years which may further adjust any input tax you reclaim initially and throughout the 10 years life cycle of the property. Same link as HMRC, section 4, specifically section 4.6 which looks at intention but you are past the intention stage as you are only making exempt supplies. HMRC will inspect the first return, they will see you are making exempt sales because Box 6 will have net sales value and no output tax in Box 1 so you should be prepared to defend whatever position you take in terms of input tax recovery, remember that the right to reclaim VAT is on the basis you make taxable supplies....what happens if your taxable part of the business is still in development 1 year from now, or 2 years from now? This is the sort of thing you should be speaking to your Accountant about.

https://www.gov.uk/vat-margin-schemes/keeping-records (you'll need to read through to the section under "selling").

Place of supply of services is (default rule) where the client is based. You don;t state whether your client is a business or a consumer but assuming it is a business/in business, then it would your sales are outside the scope f UK VAT and the customer accounts for VAT in their own Country. Outside the scope sales do not count towards the VAT registration threshold, so you could turnover £100k of sales to your overseas business client and not trigger a VAT registration, you can voluntarily register for VAT if you want to reclaim input tax incurred in the UK. There are some exceptions to the default rule, services relating to land or where performed services may see you having to register for VAT in the Country where your client is based (you don't state where your client is located in the world) and so you may need to read the HMRC guidance here https://www.gov.uk/guidance/vat-place-of-supply-of-services-notice-741a to ensure you are aware of the various rules relating to land, where performed type services.

You state you are refurbishing a house which has been empty for 2 years, you then later state that you created a company to buy the houses (plural), so that might be a typo but in essence you have acquired an old dwelling or dwellings into a limited company. What claim are you thinking of making? If it is a self-build DIY claim, I do not think that would be eligible, DIY claims are for new build dwellings, whereas you are refurbishing an existing dwelling. Also, DIY claims are meant to be made by individuals rather than a company. Companies trade and so if a company owns a property it would at some point sell the dwelling, you cannot use the DIY scheme if the intention is to develop and sell a property. If you are thinking of registering for VAT and reclaiming VAT having sold the refurbished dwelling, the sale of an existing (old) dwelling is exempt, exempt means you cannot charge VAT on the sale or rental of an existing dwelling nor reclaim any VAT related to the refurbishment and sale of that property. You don't state what your intention is with the property, but in reality you can rent it, or sell it, or live in it but in none of these scenarios is there an opportunity to reclaim input tax, only if this were a new bild being sold (zero rated) could input tax be reclaimed.

You can only reclaim VAT if your are i) VAT registered and ii) the VAT being reclaimed related wholly to a taxable business purpose. If you are VAT registered and the certification for building work is directly in relation to your business activities (ie, if you are a property developer and you are building new dwellings and you paid £300+VAT for this certification), then the input tax should be recoverable, subject to normal VAT rules (partial exemption, etc)....but you mention the certification was for your own house, so it may not have been recoverable anyway as a house has a dual personal/business purpose (if working from home), so VAT would only be partially recoverable anyway. If you are not VAT registered or not a business, you cannot reclaim VAT. This then becomes a legal dispute between you and the supplier and their liquidator.

Sounds like an indirect export, see this Notice, VAT on goods exported from the UK (VAT Notice 703) section 2.9 and 3.4 
If the German seller was responsible for shipping the goods to UK, they can zero rate it as a direct export because for the zero rate to be valid the supplier must have proof of export (shipping paperwork from the freight agent).
Where the customer arranges the shipping, this is an indirect export because the supplier does not have any proof of export, for all they know, you could have arranged for DPD to pick up the goods from the German factory and transport them to a customer in Germany and as you are paying for the shipping, the German supplier does not have any proof or paperwork as all of that goes to you.
So because German supplier has no proof of export, they can't zero rate, hence the 19% VAT charge (which you cannot reclaim on a UK VAT return).
Go back to the German supplier and explain this was an indirect export and present them your shipping documents and proof that the goods did indeed end up in the UK, with copies of this paperwork, the German supplier should then be able to satisfy the zero rating conditions and issue a credit note for the 19% VAT.
If doing future transactions like this (arranging your own shipping), it would be good to chat this through with the seller so that everyone is aligned and you get charged foreign VAT upfront and then have it refunded once proof of export is presented.

You should have listened to the Accountant and not paid the £4,487.67 because that has now complicated matters further. When HMRC do not receive a return on time, they will estimate an amount due (£4,487 in your case), and penalties and interest will be based on that estimated amount until you file an actual return. Once you file the correct return (refund of £219.71) then HMRC will cancel the estimated amount of £4,487 and also cancel any penalties and interest because penalties and interest only apply where you owe VAT to HMRC, as your first return was a refund then no VAT is owed to HMRC and so no penalties/interest due. However, the submitting of a return and the making of a payment can sometimes take a few days for HMRC to update their records, and there can sometime be even longer delays but usually VAT account will be updated within 7 days maximum. The debt chasing letters are sent automatically and will likely have been sent before the VAT return was filed because those letters take a few days to be produced, put into envelopes and posted 2nd class, so the debt letters could have been ignored as long as the VAT return was filed....it's a timing thing, you know you've sent the return, you know it is a refund so you just have to be patient and wait for things to update....I'm not saying ignore debt letters from HMRC, but you knew you had filed the return, but I appreciate that nobody likes debt letters. When you paid the £4,487.67 did you ensure that you used your VAT number as the "reference" when making payment via your bank/online payment? If you make a payment to HMRC and do not use your VAT number as the payment reference, HMRC will not be able to match the payment to your VAT account and so it might be your payment is unallocated/floating around in HMRC's bank account with no home to go to. if that is the case, you need to call the VAT helpline and explain that payment was made without reference, they may ask you to write in with a copy of your bank statement showing the payment being made and that will then fix the issue....but it will not be quick, could take 3-4 weeks to resolve. On your VAT account it originally showed you owed £4,878 then when you filed your VAT return it shows a refund of £219 (which is correct, the £4k and penalties are wiped out and replaced by the £219), had your payment of £4k been allocated to your VAT account, you would now be showing as in credit by £5,097 (£4,878 + £219) in effect you will have overpaid your VAT account by £5k but the fact the VAT account is only showing as you are due £219 then this tells me that the payment of £4k you made has not been allocated to your VAT account. If you have paid using your VAT number as reference, then HMRC may have misallocated your payment (their error), again, you need to call HMRC and explain the situation, the £4k is not lost, it just needs to be allocated properly. Trust that all makes sense, might need the Accountant to assist you or else you have enough in this post to call HMRC and explain the situation.

You can update your company name via your government gateway, you will be asked to provide proof of name change and then HMRC will update your VAT certificate in about a 7-10 days time.....and you can download your new VAT certificate again from your government gateway.

The proof of address is of the individual/person - whoever's photo ID you are using, then it is that persons home address that HMRC are asking proof of. You say you are Chinese, if you live in China/reside in China, then you would use your Chinese home address and your evidence you send to China will be for your China home address. If you are not resident (living in) in Northern Ireland, then you will be a Non-Established Taxable Person" (NETP), that is, you are not established in Northern Ireland. HMRC need to be able to prove you (the person) are who you say you are, which is why they require photo ID and proof of home address.