First: If the project was under the the GPL and the libraries are under the GPL, the result must be under the GPL.
Second: Depending on where you live, you might or might not have given over the rights to your employer. You need to take your contract to a lawyer in your country and ask them. As usual, slashdot is _not_ the place to get specific legal advice; we can just blabber about generalities.
Thing is: The GPL does not matter unless you distribute the software to anyone. Before that, the licence does not matter. So you need to check the _second_ point first. When/If you release the software and the libraries are GPL, it's a clear-cut case.
No idea if your employer can go after you for "wrongfully leading them to believe they owned this stuff" though...
You're at Witt's End.