It was that if you put a new file, it uploads a file and each file has a file-id. On the server you have the file-id in the main database and the client has a local one where changes are tracked and if there are updates, the files are transferred again.
ownCloud implemented a feature with checksum tests but I think it was only to verify that the transfer finished correctly. So you would still need to sync the files a first time, you can’t just put the file manually and the client would compare the checksums and say it’s the same file. I’m not sure if this feature was backported to Nextcloud (it wasn’t available in NC 12 and there were issues when people migrated from oC) and I don’t know if this is planned. Also ownCloud is currently testing a delta-sync. Nextcloud was not very active in the desktop client development but this is changing a bit since they plan to implement client-side encryption: Desktop client has less releases and is behind master