Schematics and PCB don't seem properly linked

I got handed over a PCB project, I have the parts libraries, schematics and the PCB. The PCB and schematics seem to only semi-correspond to each other: I can cross-probe all nets that I tried, didn't try them all) and some components, but not all of them. So I tried to sync up the SCH and the PCB, and no matter what I tried, around 180 components would always disappear from the board and would have to be placed manually again. At the same time, some of the constraints (most notably, for routing diff. pairs) would stop working. The same thing happens if I try to use the Update PCB button, or if I export a netlist from the SCH and import into the PCB. I can see no logic as to which components disappear (they are not the same ones as the ones I cannot cross-probe), but it's always the same amount, and always the same ones. 

The closest I got to stuff not going whack is by fixing/locking a few components I know would disappear, and then trying to update the PCB while unticking the "ignore FIXED propery" checkmark. In this case, the update wouldn't happen, and I would get thrown a message saying "Error processing 'C101': Cannot modify element; the object or a parent has the FIXED property.", then "Run stopped because errors were detected", then the whole process, well, stopping. 

Any tips as to why this might happen? Maybe some file got missed in the handover (it was remote, I just got handed a bunch of stuff), and I should ask for it?