Fixing inconsistency between the schematic & PCB is tricky - it is best to avoid getting into that situation in the first place by keeping both open at all times.
Having replaced the parts to the board and run a consistency check, what report do you get?
Keith.
---------- Post added at 15:18 ---------- Previous post was at 15:07 ----------
By the way, nets can only be added on the schematic, I believe, so you need to delete the connections on the schematic that don't exist on the PCB then check consistency. When it is OK, redraw the nets on the schematic. Depending on your PCB, it may be easier to simply re-create the PCB.
---------- Post added at 15:19 ---------- Previous post was at 15:18 ----------
One thing I have never done, which may work is to export a netscript from the schematic (without the PCB open). Then import the netscript into the PCB (without the schematic open).
Keith.
---------- Post added at 15:22 ---------- Previous post was at 15:19 ----------
Just tried it - it seems to work (even if you don't close the schematic/PCB). After exporting the NETSCRIPT you need to RUN the SCRIPT in the PCB rather than import it. That re-creates the connections at the PCB level.
Keith.