mate in mass-storage mode you should see the files , if you don't , isn't a problem related to tracker but rather files/filesystem/corruption/ etc

LOL now I used that very handy Windows program called TreeSize Professional with mass storage mode to find where the high use of space is located... I had somehow moved the two folders into another folder...

OK, that sounds like a file system corruption. It might be tricky to recover the data especially if you have written to the medium after the corruption had occurred. It may not be possible to recover all the data.

I recommend running some disc recovery tool on your PC with the phone attached in mass storage mode. You can also try TestDisk on the phone itself although I haven't had much success with it myself so I tend not to use it. So far I have had the best success with FreeUndelete on Windows but it may only work for files that are literally undeleted - as opposed to gone due to partition corruption etc.

I have rescued my own data in the past by attaching my phone to a Linux comupter, making a binary copy of the whole partition with dd and working on that copy.

Of course, things are much simpler if you have a backup. Just reformat your MyDocs and restore your data from the backup.

EDIT: seems like I've been beaten to it.