A couple of things:
1) When Backup Exec first queries Lotus for valid database files, there is an open / close attempted on each one. If for some reason Lotus doesn't report to Backup Exec that certain .nsf/.ntf/.dsk/.box files are valid databases, we put them in a skip list so we don't attempt them again. Sometimes just clearing out the skipped list is enough to get the DBs added back in the job or selection view. Steps for clearing out the skipped list:
A) Stop The Backup Exe Services (both local and remote this applies)
B) Move the Noteslbd.txt, NotesDB.LBD, and NotesDBC.UCJ files out of the Backup Exec Logs directory
C) Restart the services and try to create/run another backup.
2) If you have the Lotus agent licensed/installed then files with .nsf/.ntf/.dsk/.box extensions are not attempted during the file backup. They are automatically excluded.
Russ