How to periodically sync without wiping out server-side files

I have a small QNAP NAS on my local LAN and SeaFile hosted in a VPS. The way I want to use SeaFile is to have several directories on my NAS sync up to the SeaFile server. Right now, I don’t have an easy way of running the sync client on the NAS, so I was thinking I could mount these NAS shares on a local computer and then run the sync client there. The problem is that I won’t always have these shares mounted. I don’t want the SeaFile client on my laptop to see the missing NAS mounts and delete files on the SeaFile. Since I can’t run the sync client on my NAS, I guess I don’t care if the SeaFile server isn’t in sync with the NAS immediately, so I would just run the sync client occasionally to push the latest up to the SeaFile server.

Has someone done this sort of thing?

I sync to a NFS share using SeaDrive on a linux machine. I guess I would ask what software you are using to sync. I use rsync which you can set to not delete files that are no longer present on the source.