It's tricky. What would have been best if customer and author had figured out what exactly they want, and a contract had been signed to specify that. As it is, there are lots of unknowns; I would suggest the author should ask the company nicely for a gpl-licensed copy of the code and he is mostly in the clear (mostly because he is not the sole copyright holder anymore); if people get angry then in the worst case this ends in a costly court case. So be nice to save lots of money.
First, under which license did the company get the original software? If the author is the sole author or agrees with the other authors, it could be any license, including obviously the gpl. Whether the company downloaded the software themselves doesn't really matter, the copyright holder can always give permission to use a different license. I know of one case where a company ordered software with the intent to have all rights to the software, the developer gave them gpl-licensed software, and had to pay damages because that was not what was in the contract.
Second, who has the copyright on the changes? In the case of "work from hire" most likely the company that pays. But something that could be argued about in a court.
Is the company distributing the software by hiring someone to modify it? That can be argued for and against. Very good for increasing court cost. Obviously the author will have no rights until the software is distributed, so that makes a difference.
What if the author makes a copy of the software with his changes? He has no right to do this. Even if the gpl forced the company to give someone source code, that doesn't give anyone the right to take it.
So the author is fine if (a) the company understood that the delivered software would be gpl licensed, and (b) the company voluntarily allows the author to take a copy of the modified software.
All this is much better handled beforehand with a contract. And if there are disagreements between company and author, you'd have to be very careful to avoid ending up in court.