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Sorry to hear you’re facing problems 
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Nextcloud version (eg, 20.0.5): 20.0.4
Operating system and version (eg, Ubuntu 20.04): FreeBSD 13.0
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The issue you are facing:
Originally I had the nextcloud service running, but it had some issues, so I had to do a clean install and re-setup the SAML authentication. When I reconnected my account from the server to the client. My expectation, was that it would present a prompt to choose the file and folders to sync. However, It just deleted all the folders and files that were not previous synced from the last configuration and non-existent in the server. It also synced files and folders that had client to server sync enabled in the previous configuration. Is there a way to reverse the sync from the client side. Those files are no longer stored on the server as it’s a fresh install. And I cannot perform a roll back from the server side since those snapshots are gone as well.
Is this the first time you’ve seen this error? (Y/N): Y
Steps to replicate it:
- Re-create server and setup SAML
- Sign In To Nextcloud
- Click Sync Files
- (No prompt to select files and folders to sync.) Last time I setup an installation, it did prompt the option to select which folder you wanted to sync from the server to client. It used the last time client configuration instead of prompting to select the files and folders again.
It looks like Nextcloud client just deleted the files and folders. I’m not sure if it stored an extra copy in the server somewhere or moved files into the Trash on the client side?
The GUI client tells you exactly what files and folders were deleted.