Zorian,
The only thing I can think of is that he's talking about is in Administrator | File | Configuration | Templates and the Paths tab, but that info is stored in the registry and won't change.
In all of our client updates, we had them do a backup of the database in Manager | Utilities and copy the Reports, Labels, and CrystalReports folders somewhere else for a backup.
Then uninstalled RMS in Control Panel | Add/Remove Programs | re-start the computer | slip in the 1.3 CD, install, and re-start again. It will find the dongle again on restart