Is Vali-Flash and Vali-File compatible in terms of the valisig.dbf database?
Vali-Flash 3 and Vali-File 3 can use the same database. Just note that when you copy the files over they can not be in use unless you use the database backup and database restore. Basically what this means is that the databases (valisig.dbf) are in use while the program is in use. The backup/restore option closes the database before doing their respective operations. Both Vali-Flash 3 and Vali-File can be running simultaneously.
One thing you might notice is that the Device database field will say "File" for any file operation and in Vali-Flash you will see "CompactFlash File". In Vali-File you will see the just the size of the "device" from Vali-Flash. This is due to the size limitation of the device field. But you should not experience any problems. As always make sure that you make and keep backups whenever you add/change games as general backup procedures recommend.
Vali-Flash 4 uses a different database from Vali-File and Vali-Flash.