No, Traktor only saves data which can be stored in the ID3 tag in the MP3 (like artist, title, …), but all the rest is saved in collection.nml, namely hotcues, loops, beatgrid and playlists. So the only difference is that Engine does not store changes in ID3 tags to the MP3 file.
So in Traktor you would have the same problem, but you can fix it in the software with the relocate function…