When setting up my new Samsung phone with Smart Switch it automatically copied all my camera photos etc as well, which is probably the case with most “phone transfer” type applications. When I then went to setup Nextcloud of course I got hundreds of file upload conflicts because files that were previously backed up were again found on the phone. As conflicts need to be resolved 1-by-1 in Nextcloud this would have been an impossibly tedious task to go through the conflicts one by one. There is an option to set a default behavior to skip upload when a local file is already on the server, but unfortunately changing that setting doesn’t affect the existing queue of hundreds of conflicts. In the end I had to uninstall nextcloud on my phone, then reinstall and when setting up Nextcloud’s auto upload, be sure to set the default to “skip upload” for every folder to be synced.
To save others from a similar issue, the message is simple: when setting up Nextcloud auto backup on a phone that was setup with Smart Switch or similar, be sure to not just “click the cloud” when selecting folders to auto upload.
Instead, for each folder click to 3 dots, select “Configure”, then toggle the Auto Upload and change the setting “What to do if the file already exists” to “Skip Uploading”. Then click “Save” to turn on auto upload for that folder.
Your folders will sync without conflicts for those files that were already uploaded from your old phone, and new photos will still be uploaded as expected.