Interesting. My volumes were similar and I even had issues with my 'beefy' enough DO VPSs. The primary issues for me were with the clients, especially if I, say, moved a folder of 2000 files from one directory to somewhere else within the Nextcloud drive using the UI. Anyway, I'm not here to troubleshoot that - I've long since decided that it's just too much for my personal simple use case of keeping two folders in sync with each other on different devices. Out of curiosity, how did you install Nextcloud? Snap/Docker/Manual?
Ah, during our migration we did try to move thousands of files from a "Dropbox" folder to a "NextCloud" folder, and indeed the Windows client was not happy. Since it was a one-time thing, the solution was to move the files "manually" over SSH and just run the NextCloud "scan" utility to pick up the changes on disk.
I'm running NextCloud via the official Docker image, reverse proxied through nginx.
My good old friend, the Nextcloud scan utility :) I lost count of the number of times I ran that and the trashbin cleanup. These are both problems I never ever want to have to deal with.
eh, I ran the command, alt-tabbed to something more interesting, and checked later in the day to see that it was done. Never had an issue running it, and only ever needed to when I was doing the initial data migration.