Ludwig, VAT office may be pedantic but it's not stupid. They'll suss you out and recliam their tax with additional interest. Also, abuse of the system leads to it being changed to the detriment of legitimate claimants. This is what happened a few years ago when Gordon Brown decided that a system that allowed trainees to make tax claims against costs for flight training (and diving and sailing etc) would be abolished as folk were taking the piss. Cheers to those that took the tax credit but didn't actually intend to become professional pilots, it's meant that subsequently it costs an extra 20 grand to become a FI (H) as compared with costs 5 years ago.
Rotormad, you're right in that you would likely have to really go through the mill with HMC&E if you have employee status in respect of one job with the company for whom you wish to freelance in respect of another. That said you might still pull it off if you explain clearly the situation and the VAT officer is open minded to your explanation (not likely). Alternative sources of income should not conflict with a wholly separate business claim.
Go-around, the VAT office may wish to claim back a proportion of the VAT repaid if you end up becoming an employee of a company soon after being free lance. Same applies if you don't make any VAT returns after claiming VAT back i.e. don't work and therefore don't earn anything. There's no hard and fast rule for these situations, which do arise of course. It depends on the credibility of your circumstances and the zeal of the VAT officer concerned.