You would so get a worser sound quality, since you need to uncompress and then compress again. So never good to convert to other formats (only you "only" would use with small devices).
You cab use Winamp to convert them to all wav files (using discwriter as plugin), and then use cdex to compress them again to a other format. Im known this is not the best option, but it work. Both of them should support subfolders as well.
But you should stick to that format, you originally compressed to. If you have them on cd's, it better to rerip.