I have identified that the Database Compare tool if "closed" before it completes Analyzing Matches leaves the program in an unintended state. The Compact Database tool aborts because of the SQLite 1 error. Closing the database causes an Access Violation. From the persistence of SQLite "journal" files that are supposed to exist only for the duration of a successful SQLite transaction, it is apparent that both the main file and the DUP file are left in mid-transaction.
It is probable that aborting Database Compare is not the only cause for these errors to arise. It is advisable to let Database Compare complete its analysis or to avoid using it altogether if you want to reduce the probability of these disconcerting errors.
I have communicated my findings to RootsMagic.