You can & should do some type of validation on your databases prior to an upgrade. Here is what we have done in the past before performing an upgrade.
a. Get a clean BackUp.
b. Check health of the network OS.
b. Run a validity check on the GW databases.
c. Perform a Top Down Rebuild (If Necessary!!)
d. Perform GW upgrade.
Validating a database can be done through NWAdminxx or through ConsoleOne. Just remember, once you get to GW v6.x DO NOT use NWAdminxx for your administration, only ConsoleOne. Using NWAdminxx on a GW 6.x system can and will cause database problems. The upgrade is straight forward as long as you prepare your system and have a good upgrade plan. Is it just me or did my last statement sound like it was said by Homer Simpson? Anyway, good luck with your upgrade, you will thoroughly enjoy the benefits of the 6.5.x system.
FarOut
V-Peace-V