The next cloud android app is particularly bad if you use it to back up your cameras DCIM directory then you delete the photos on your phone. It overwrite the files on Nextcloud as new photos are taken. I get why this happened but it is terrible.
it's bad for everything.
i have lots of txt files on my phone which are just not synced up to my server (the files on the server are 0 byte long).
i'm using txt files to take notes because the Notes app never worked for me (I get sync errors on any android phone while it works on iphone).
Will this also happen if you let the Nextcloud app rename the files as it uploads them? I usually take that option and haven't had an issue with this although I don't have it set to delete from my phone after uploading.