I installed Nextcloud Desktop on windows and connected it to my server, however the default folder where the client syncs already had some files from a previous try at setting up the server, so when I connected it, the Desktop client deleted all the files in the folder.
How do I get these files back?
Easy to answer: Restore the last backup
If you wanna get a more detailed answer you n eed to deliver more detailed infos. From what you wrote so far i don’t even know on what device the file was deleted.
Was the files deleted on the windows client device or the NC-Server? You did not make that clear.
Restore these files from backup. You do have backups, right?
Also, if you have the Deleted Files app enabled on your server, it should be enabled by default, I think… then try the Deleted Files feature on your Nextcloud web page.