hi ray
to answer your question, yes rekordbox analysis will overwrite tractor/rekordbuddy analysis so you should turn it off if you want to keep your grids intact.
you are right, traktor grid analysis is the best but i think you'll find rekordbox 3 much improved from v2. i used to use the same traktor > rekordbuddy > rekordbox process as you but after testing out rekordbox v3 i found it to be almost as good and now use rekordbox exclusively.
try testing it out on the same 20 or 30 tracks with both software and see how it works for you.