Veeam support send me the hotfix yesterday (less than 1h after opening the case).
Since I installed the hotfix, all backup jobs ran 2 times on our offsite Synology NAS (DS1817+).
We got 6 backup jobs (2 Linux Agent Backup + 17 VMs).
It worked flawless. So, it seems the issue is gone after applying the hotfix.
BTW, the backups are much much faster with the "Linux" server repo type, than in CIFS mode!
I will wait few days more before closing my case (just to be sure). I'm a happy customer.