Welcome, rschip2.
As I understand it, there's no issue to be fixed. Unfortunately, if a database has been damaged by an early beta, then the damage is done and there's nothing the program can do about it. But what do I know... maybe it should detect and repair damage done by bugs in previous versions.
There's still an issue, of course, but I'm not sure what should be done about it. Some like to live dangerously and use their only database in a beta without making backup. More are in the same situation as you—you made backup, but didn't realize your active database was damaged in this particular way for an extended period of time. I've done it myself.
Perhaps the program should be stricter about using databases from different major versions. It could automatically make a backup of a prior-version database before converting it, and refuse to open any database that has been opened in a subsequent version. The same thing could be done for any particular minor revision, if the risk was deemed high enough (e.g., early betas, where "big" changes are being made and bugs may not be found immediately). In hindsight, you would have been better off had you been forced to revert to your original database (i.e., that "untouched" by 0.9.9.x) when deciding to go back to 0.9.8.20.
If it weren't for this particular, perhaps unlikely problem, such precautions might seem like overkill. After all, database formats often change when a major revision is made to the program that creates them—so it's not possible to use the same database in different versions anyway. But it might be an effective way to prevent this sort of thing from happening again. It would also save users from themselves should they be so eager to try a new version they "forget" to make backup.
