Your best bet is to open 2 Designer instances, one with the PLC project (opened via the COMM LINK), and one with the DISK project. You will need to do a PLC->Disconnect on the ONLINE one so that the DISK one can re-use the link (or if it's Ethernet, create a NEW LINK and use the NEW link when opening the PLC project).
Then use the PROGRAM Designer's COMPARE on the DISK project to navigate the differences, and copy/paste/whatever those into the PLC Designer.
You will want to do a SAVE-AS to disk of your PLC project and call it something <original name>_ONLINE_EDITED.dmd