AAC is lossy, of course. So what comes outa the decoder ain’t gonna be bit-for-bit identical with the original going into the encoder. But FLAC and any other lossless codec should be bit-for-bit. If it is not bit-for-bit identical, then a glitch happened somewhere, but alpha and beta testing should have uncovered any bugs that would do that.
If a lossless coding algorithm is working, the worst you can toss it is broadbanded white noise. It will likely not compress at all. Some algs might result in a “compressed” file that is longer than the original.