Errors when Syncing folders after switching servers from production to replication server

When Syncing Seafile with the main server there are no issues.
When switching on our replica server which is a like for like a server with the main server.
Conflict files are produced. And the server fails to connect back to all the folders.

We have experienced the issue several times when connecting to the server.
How can we ensure when switching on one server with the exact folders and files are conflict files created?

How to prevent conflict files?
How to ensure that all folders are automatically synced?
How to check that both servers have exactly the same folders and files without searching through.