you retried with gallerybugx thing? with new deb? then yes, old deb contained gallerybugx that was actually bricking things because i had to brick my phone before i test fix, but i tried to pack real thing and qt B i t c h packed bad gallerybugx and it was your ghost
kill me hihihihi
glad it worked, yes, i am sure your contacts are buggy, they should be there, and tracker think that they are updated but they are not in database.
i am not tracker magicman and maybe arie know more about this.
i had that too and i fixed it by restoring backup (that changed contacts contents and tracker tracked it (same with messages).
so you downloaded emmc.bin?