You'd need to load VFS configs for WF607 and AFS, create an item mapping between them open the map converter and load the mapping, and then load each map into the converter and save it. Or at least all the maps where you think there might be incompatible items, so probably all towns, SAMs, caches and other interesting sectors. Just uh... Make sure it works after you do a few maps, it definitely should but it's still an early version so better safe than sorry.

If that sounds like too much manual work, I can try to add some sort of bulk processing option to the map tool, although that would probably have to wait until the weekend.