Unless some authorities make the case that one's intent was to remove it and they just failed in that attempt.I am not a lawyer but it seems that if the serial # is still legible or can be rendered legible then it really is no a problem.
Most serial numbers can in fact be deciphered through forensics even if they are filed off. Some agencies like the BATF even specialise in it.
If you resurfaced and polished it and then etched the serial number in better, or engraved it a little more and it is the appropriate unaltered number there should not be a problem, and it won't appear someone tried to remove it.
If you pursue this as a legal issue the firearm will likely be confiscated as evidence (especialy since it is in fact the case), and they may or may not return it at a later date citing the "removed" serial number as a reason.
I hope the choices you make work out for the best.