You should not expect a project to disappear without a reason, such as deleting the project by API or taking away read permissions for the user trying to see the database.
ElectricFlow does not need to perform a synchronization with the database. While some API calls do get added to a queue for processing (such as running a job, or starting a delete operation that may take time), there isn't a synchronization that is necessary.
In commander.log, if you see the API call to deleteProject, there is your evidence.
Alternatively, if you see a call to modifyAclEntry, createAclEntry, deleteAclEntry or similar, that may explain why a user can no longer see the project. Remember - if you removed permissions to the project, you may not see the revision in change tracking. User admin can revert those types of changes, but not restore a project that was deleted.