You may need to clean the databases then... start with the one that seems to be the cause of the problem. Do a fresh backup, then open "MiVoice Office Database Utilities", open the database and select "Repair without prompt" then Test. It will extract the database, prompt you for the username/password, do a full test and repair or remove any invalid entries and display those changes, compact the database, and re-write the backup file. Then do a restore to that node, if that fixes it your done, if not, continue through all the other sites. If you still get the error, you missed something in your combing.
Then again... if it isn't affecting anything and it's just a bothersome error, maybe it's not worth the trouble. I have seen many networks that have several conflicts, and it is rarely a user affecting issue.