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The third party Accountant did not need to be assigned as agent, they could have filed the VAT652 online using just their email address.
https://www.tax.service.gov.uk/submissions/composite-auth/auth-selection-form/notification-errors-vat-returns?continue=%2Fsubmissions%2Fnew-form%2Fnotification-errors-vat-returns
HMRC will write to you as the taxpayer, I would also expect HMRC to reply to the tax agent who filed the VAT652 (the third party agent), but you should also disclose this error to your usual Accountant or else when the usual Accountant comes to do year end accounts and VAT return reconciliations, nothing will balance as the VAT652 is dealt with outside of the VAT return quarters but your bank account will show a large refund coming from HMRC which will not match to the VAT returns.
Timescales to process is variable, can be between 1-3 months, but if many NETP marketplace traders are now suddenly submitting VAT refund claims, then you can see that HMRC may be very busy with these claims and so a delay in processing is to be expected.
I would expect HMRC to enquire into the detail of your refund and so the delay you are having is probably because your refund claim is waiting to be allocated to an Officer who will then contact you and request evidence and documents to justify the refund.
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Useful thread with a similar query - https://community.hmrc.gov.uk/customerforums/ie/7d83f3c0-7f5b-ee11-a81c-002248c8c17d
You will likely find that you require a German VAT registration. When you zero rate the export of goods from UK to Germany, those goods will be subject to German VAT at point of entry/German dockside, someone has to pay this German import VAT, either you or German retail store.
If title remains with UK at all times (until the goods are sold in the store), then logically only the UK entity can be the importer of the goods as they are your goods and you retain ownership of them in Germany. In other words, you make a zero rated export in the UK and you are also the importer of the goods in Germany and liable for German import VAT.
When the retail store sells your stock, what is actually happening is you sell the stock to the retail store first and then retail store, now owning those goods, sells to the store customer.....so this likely means you need a German VAT registration because you own/hold stock in Germany and you sell that stock./goods in Germany, it is a German to German supply....as a UK entity, you are not established as a German company in Germany, therefore VAT threshold in Germany is Nil for non-established businesses, UK entity registers for German VAT, charges German VAT on stock sale from consignment to retail store. UK entity also acts as importer of the goods into Germany, reclaims German import VAT on German its VAT return.
Remember, the place of supply of goods is where they are at time of sale, the time you sell the stock is when you sell it to the retail store and where is that stock? It's in Germany, not the UK.
HMRC are unlikely to be able to advise you on German VAT or EU/German rules, so you should speak to your Accountant or liaise with your freight agents/couriers to better understand the implications of importing goods into an EU member state on a consignment stock basis.
HMRC do not seem to have any guidance on this (other than pre-Brexit/prior to 2020 guidance which is no longer applicable), because this forum does not approve of external links (for obvious reasons), then Google "consignment stock, 2021" which should produce several links for you to explore.
When unsold stock is returned, it is important it is sent back to the UK under an appropriate customs code so that it is not subject to UK import VAT, another reason why to speak at length to your freight agent/courier as well as the retail store as they are likely the ones arranging return shipment and if they do not use the right (Customs Procedures Codes) CPC's when the goods are exported to Germany and when they are returned to the UK.
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There can be delays between submitting a VAT refund and receiving the VAT refund.
HMRC perform a variety of checks on VAT returns, if this is your 2nd or 3rd refund, then HMC may want to inspect your records to check everything is correct. once your return has been selected for review then it is allocated to an HMRC Officer who will then decide how to proceed - they may call you, write to you or email, depending on what information you supplied when first registered for VAT.
This allocation for review process can take up to 30 days but HMRC will often contact you before that timeframe, refunds will not be released until HMRC have performed their checks, so once HMRC contact you, it may still take another 7-10 days to conclude the review, depends on how quick you are in replying to HMRC queries.
In terms of current turnaround times, I've not seen any particular issues with my clients with refunds, but refunds can sometimes be delayed if HMRC are short of staff resources (eg. holidays) but if you are regularly receiving refunds then it is almost certain that you will get an enquiry within the first few VAT returns, all you can do is wait until HMRC contact you....and check on your gateway that all your contact details are upto date...and if you are based overseas and HMRC have to write to you, that may take 7-10 to reach you, depending where in the world you are located.
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Your analysis of the UK VAT return are correct.
Boxes 1 to 5 are exactly as you state.
Box 6 should only contain the value of sales made to UK B2C (consumers), the sales you make from Sweden to UK businesses (B2B) are reverse charge and those are declared on your Sweden VAT return only, not the UK return.....remembering that we only need to record UK B2C sales on the UK VAT return as the place of supply of digital services B2C is where the consumer is, but for B2B sales, the place of supply is where the business is but that the business accounts for VAT under reverse charge.
Box 6 should not include your domestic Sweden sales or sales to other EU member states/rest of the world., all of those sales are detailed on your Swedish VAT return,
Box 7 only concerns itself with purchases made in the UK, as you are not buying anything in the UK, then Box 7 should be Nil, same as Box 4. With regard reverse charge on purchases, I can't think where a Sweden based "digital newsletter"business would be buying in a a service subject to reverse charge....for example if you have a contract with Google or PayPal, these are services based in Ireland and their contract would be with you in Sweden, reverse charge applies but would be reverse charge on your Sweden VAT return.
Boxes 8 and 9 are only ever used if you are buying or selling physical goods from/to Northern Ireland, which is highly unlikely if you are only selling digital services.
Your conclusion of deregistering for VAT makes sense but is a business decision for you to make, for just one (or possibly two) sales per year then it may be much easier to block customers from UK buying, I have client in both UK and EU who block certain Countries in order to avoid the headaches of registering for VAT in another Country, although the EU does operate MOSS/One Stop Shop which does at least make it easier for a digital business to charge VAT to other EU member states without having to register for VAT in each memberstate.
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You can't reclaim German VAT on a UK VAT return, to reclaim German VAT you would need a German VAT registration....so you would need to factor in the irrecoverable German VAT into your pricing/when calculating your profit margin.
Your invoice to UK customer would be subject to UK VAT, place of supply of services rules https://www.gov.uk/guidance/vat-place-of-supply-of-services-notice-741a#sec9
indicate the place of your supply is where the customer is, customer is UK and so UK VAT applies (20%) to your invoicing and you declare the output tax on your UK VAT return.....but you cannot reclaim any German VAT at all on the UK VAT return.
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TOMS is still applicable post Brexit.
https://www.gov.uk/guidance/tour-operators-margin-scheme-for-vat-notice-7095
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If you (UK company) has bought goods in EU and those goods have been exported from the EU to China (or anywhere), then you (UK) appear to have purchased goods in the EU, the place of supply of goods is where the goods are at time of purchase....so the EU supplier will charge you EU VAT which you cannot reclaim on a UK VAT return, and the UK company has likely triggered a VAT registration in the EU member state where the supplier is located.
HMRC are correct that your UK sales to China/elsewhere end customer is outside the scope of UK VAT, but this is because it is subject to VAT in the EU somewhere.
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Have a read of this guidance from HMRC's internal manuals.
https://www.gov.uk/hmrc-internal-manuals/vat-flat-rate-scheme/frs3300
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Your turnover is the value of your sales.
For example, you sell something on eBay for £12, that would be £10 net and £2 VAT (if VAT registered), so your turnover for VAT registration purposes is £12.
You receive into your bank account £9. which is the fees you pay for commissions, listing fees or credit card charges. These are your expenses/costs but they are not your turnover, your turnover is still £12.
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If the Director of the UK company is not resident in the UK (this means no management or control of the business takes place in the UK) and if the company does not have an establishment (address) in the UK, then the UK company is not resident for VAT purposes.
You cannot use the address of a registered office or Accountant or agent, established means you either employ people in the UK or you have an office or premises which HMRC can visit and perform a VAT inspection at.
https://www.gov.uk/hmrc-internal-manuals/vat-registration-manual/vatreg37150
You are asking if you can change your address to a UK address, that can only happen if the UK address is not a virtual or registered office or accountants/agents office.