Yes of course! No worries and all sorted now anyway, so just did extra flying I would have done anyway... But for the OP I think there will be a fair amount of complication with his application, unfortunately.
It does seem though from what Nick said that the exemption may not have additional clauses on it if applied for before the skills test (this may have just been my added complication!)... So I guess the answer to the OP is: you can use those old hours if you are able to justify them on the exemptions form, but it'll cost you £53.00