One alternative would be to get a solicitor to draw up a contract stating that the deposit is refundable in the event of the paperwork not being forthcoming within a specfied length of time, but enforcing the contract if it came to the crunch, might be difficult and end up costing more in legal fees etc. You could also specify that the money should be held in an escrow account though rather than being paid to the owner.
I think that there is likely to be a cost for the paperwork.
If you mean he needs the deposit to cover those costs, well my heart bleeds for him but that's his repsonsibility, not yours.
It seems odd that nothing was issued prior to the works being carried out and now it seems they are applying retrospectively, although with this being Poland, maybe not so odd! I personally wouldn't pay a deposit on such a property.