Ive had the same issue and have devloped a proper work around for this:
If you are using a windows based laptop Itunes is a little buggy.
First off i suggest if you are going to use the smart playlists in itunes…use the grouping field to create your smart playlists. the reason for this is that Traktor does not use the grouping field BUT traktor will still show the playlists created in itunes, through the grouping field.
2ndly itunes does not “erase” the comments made in traktor…its just that itunes doesnt update them properly. Always do all your comments and editing within itunes or Mediamonkey or something like that.
Once you have done any type of changes in itunes or any 3rd party program, you will need to do consistancy checks on your playlists to show all the updates.
Itunes is still really buggy for id3 tagging and such so it is much better to do all your editing and such with a program like Mediamonkey then use itunes to create your smart playlists then import into traktor as a playlist.
It adds a few more steps but then you wont ever run into issues of itunes “erasing” things.