I have an Altium Designer project with a PcbDoc and a SchDoc file. For some reason a few nets (connections) in PcbDoc are not present in SchDoc. Can I update SchDoc from PcbDoc so that schematic connections (wires) would be added automatically?
Yes, from the PcbDoc file, just click on Update Schematics from the Design menu.
It will suggest you the changes to apply, and you just click on execute changes.
Beware that it will just add the missing connections with net labels rather than pretty wires.