Sorry for the trouble this is causing and the confusion! The specific cause of that error message in the thread you linked to should no longer be a problem, but there are other sets of circumstances that can result in that message appearing.
As one example, that message sometimes appears when backup software that doesn’t know how OmniFocus databases work restores a bunch of extra files to your database. That essentially piles multiple databases together on top of each other. You end up with a database that has more than one “root” transaction, none of which can reach all of the “leaf” nodes at the other end of the tree. OmniFocus no longer can understand the database, so it presents the message you saw.
In any case, you’ll want to contact our Support Humans at email@example.com ASAP - they’ll be happy to work with you to determine exactly what has happened and help you recover!