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Before using borg I would recommend you to take a look at restic. In my opinion it is better in everything than borg.
As for how to backup the database, my advice is to export the database to a SQL file and backup that file. That will always be easier than having to deal with agents that connect to the database.
As for the number of repositories, if you use restic, a single repository is enough. Besides, as restic does deduplication, if you have the same files between your machines, they will only occupy the space of one. ;-)
I hope I have helped you with some of my ideas.
Best regards.
Thanks, indeed, restic looks interesting!
For now I don’t have much use for the deduplication as every servers are hosting different data.
One drawback I can see is the memory usage. My raspberry only has 2GB I’m not sure if this is going to be an issue. Currently the data I need to back up are around 100GB.