This can be done individually for each instance.
First make sure the new backup location has the same ownership as the instance (such as the amp user on Linux). You should also have separate backup locations for each instance (subdirectories are fine), so that backups don’t mix.
Then edit LocalFileBackupPlugin.kvp in the instance’s datastore, and change the location in Storage.StorePath= so that it points to the full path of the new backup location (ending in /).
Finally, restart the instance.