I wrote this post for NI user forum, but I found this while trying to solve my situation and your questions lead me to solution, so I figured I’ll post it here as well, I think it also answers some of the stuff you asked about 
So I had this nightmare situation last night, for some moment I felt totally “alone” in that not knowing what to do, but everything’s solved now, I hope this might help someone
Had Traktor 2 installed for a while, as always, keeping my collection proper, grids, cuepoints, tags, playlists, gridlocks - all done for every single track.
Here’s what happened:
a couple of days ago I accidentally opened Traktor 1 instead of Traktor 2, both icons still in my dock next to each other. I remember Traktor 1 started to analyze some tracks, which seemed ok to me, I always analyze everything right after I post it in tractor music folder, set the beatgrids etc. I was just wondering if Traktor 1 will recognize the grids, cues etc I’ve set in Traktor 2, so I let it do his thing and did not interrupt. When done, I realized that Traktor 1 did not recognize a shit, just put the autogrid for those new tracks I had imported while on Traktor 2. well, whatever. shut down Traktor 1.
I open up Traktor Scratch Pro 2, everything looks fine, grids locked etc. Only when I load the tracks in the deck, I am starting to realize than all my beatgrids are gone. Right when I load a track into deck, the gridlock mark disappears and I don’t see any of my cue points anymore, just the autogrid, which is off in most cases anyways.
I scrolled down to see how many of the tracks have lost their grids, and turns out I’ve lost everything I’ve done in Traktor 2 since the upgrade from Traktor 1. only the playlists and preferences intact, files themselves also present, but no grids, cue points etc. 2months work just gone.
Ok then. I tend to think the accidental opening of Traktor 1 did this mess. I go into Time Machine, look for a date before that, copy the Traktor 2 folder, even the preferences from library, everything traktor 2 related to my desktop. Then I copy all this backup into my usual Traktor 2 location - in my home folder/documents/native instruments.. still nothing. the only difference now is that I can clearly see the messed up tracks, they have no gridlock mark anymore.
Then I went into Traktor 2 preferences, and changed the root dir from my usual location to the newly created folder on my desktop, where I copied my backup from time machine. open up T2, everything looks normal again, gridlock marks intact etc. Start to load files into decks, gridlock marks goes missing again, no grids no cue points, nothing.
Only then I remember reading somewhere that Traktor stores all that grid, cue etc info into actual music files themselves, so I figured I have to copy the actual files from the backup, not the Traktor software related files. Copied all the mp3, wav etc music files from last two moths from the Time Machine to my desktop. Opened up T2, in preferences added my newly created folder on desktop to Traktor music folders, also deleted the “messed up” tracks from my usual music folder, run consistency check, of course had all those deleted file shown as missing, removed missing files from collection, reimported the newly added folder on desktop with files from backup - and voila !!! had everything back just like it was. Grids, cue points, playlists, prefs - everything.
SO - do not let Traktor 1 analyze the Tracks you have done in Traktor 2, better not open Traktor 1 at all after you’ve been using Traktor 2
it will fuck up everything you’ve done.
There’s just one thing I still can not figure out. Did not want them tracks lying on my desktop, so I put those backup tracks from my desktop back to the normal tractor music directory I’ve used all the time. When I reimport from there, I still have grids, cue points etc missing for quite a lot of files, about 15-20% of the files in question. If I reimport exactly the same files from my desktop folder, where I copied them straight from Time machine, everything is fine. So now all my tracks from last two months are still lying on my desktop, so that I not lose the grid info, if I would put them back where they’re supposed to be - in my tractor music folder… now why is something like that happening ??
MacBook Pro 5,4 , Core 2 Duo, Mac OS X 10.6.8, Traktor Scratch Pro 2.0.3
Hope this helps to someone 