By MP4, do you mean MP3? If your files are MP3 or WMA (and possibly one or two others; not certain) then the Sony software (Itues equivalent) should be able to re-code them if neccessary. However, it should only be neccessary if your files are not MP3 (ie. WMA or AAC, etc.) as new Sony players can play MP3 as well as Sony's usual Atrac files.
Basically, if they are MP3, then it's fine. If they are WMA or another format, you might need to change them. If they are AAC then you'll need to use Itunes before you uninstall it.