I misread your first post, I had thought you were talking about audio files for some odd reason. But yes, splitting VOB files by separating the audio & video can result in out of sync. Not the best way of dealing with VOB files. But in your case you said you obtained it with it being out of sync for one of the vob files.

Converting to and from mpeg 2 to another such as mpeg 4 then back to mpeg 2 (DVD format) will result in loss of quality at each step since mpeg is a 'lossy' format, it throws away information to help it save & reduce file size.

A handy video tool I sometimes use is MPEG Streamclip but is most useful if you have QuickTime with the QT MPeg 2 codec. Please read the windows or mac information before downloading this program as vital information is included about Quicktime or quicktime alternative.