alfabob,
You can do one of two things.
Move the contents of both cards off of eachother and then onto the opposite card
(recommeneded through a PC card reader rather than ActiveSync
)
-and/or-
Follow CESDH0010
http://www.hpcfactor.com/support/cesd/h/0010.asp
Hard code the storage card mount point names "Storage Card" "Storage Card2" to the opposite CF card. That will prevent accidental name changing, and will allow you to swap the mount order just by assigning Card 1's name to Card 2 and vice versa.
You can remap the links, the main problem is the start menu shortcuts, which can be re-written if you alt + tap them and select properties.
The registry... generally speaking so long as there are no registered file types for an application it'll be happy enough. If there are, you may need smalltweak or the like
(or a registry editor
) and go through and remap the file pointers.
Failing that, you could simply reinstall the app's onto the new CF.