Just to clarify, what that is referring to is after encryption, none of the addresses used for change will have existed in the backup that was made prior to encryption.

But that doesn't mean the old backup has no value after encryption.   Encryption only flushes the key pool, it doesn't touch any bitcoins that were in the old wallet.  Only spending those coins after encryption would cause the change to go to new addresses that didn't previously exist.  So the old backup could still have some or all of the coins yet.

Of course, the encrypted wallet should not be missing anything, so like CIYAM suggested,  -rescan

Then if things still don't add up, look at the transactions to see if there are any that shouldn't be there.