In your backup task, simply drill down in the folder tree to select only a few folders amongst the whole set of folders you would like to backup in order to keep the backup size and time reasonable.
When the backup task succeeds, edit the task and add a few folders more.
Then relaunch the backup task.
The Synology Hyper Backup service will only backup the freshly added folders and data that has changed from the last succeeded backup task.
Reapeat that operation untill all the folders are backuped.