ex-employer wants me to invoice for work done whilst employed

Hello, 6 months ago the product I was working on got bought by another company, and along with 2 collegues I was TUPEd across to the new company. As part of my contract I was entitled to 5% of the sale of the product. There have been some inconsistencies in how this should be paid and unfortunately shares were never properly registered with the company's house. It was then agreed that it would just come as a bonus for the work done over the few years the product was created at the original company. The director of the old company is now saying that we must invoice him for services to do with the transition on the product to the new company. Since it's >£90k it would mean that we would have to register as VAT businesses for this one invoice we would also have to pay all the national insurance on this. I'm concerned that this is the incorrect way to be paid, as since the TUPE I. have not done any work for the previous company and this is a bonus paid for work done whilst employed. I think therefore should be paid through PAYE as an irregular payment and more importantly the employer should pay their national insurance contribution on it too. I think this might be a way to avoid paying NI and then also writing off the payments as VAT expenses and gaining a lot of tax back. I realise the situation is relatively complex but would appreciate some guidance here. Many thanks

Hi ,
 

It would be down to the employer to decide how this money is paid and they may wish to seek legal advice on how to do this, however if it was agreed that it would be classed as a bonus then it would just go through PAYE . Thank you .