You have to see multiboot on this type of boxes as boxes having multiple boot disks, similar to having multiboot on a PC. So each operating system runs independent of whatever is installed in other multiboot partitions.
You do have to be careful with things like autobackup, especially if you use other images that are OpenPLi derivatives, as they may write the same files to the same directories on your harddisk or USB device.
For multiboot partitions you need multiboot images, if you flash a standard usb image, it will wipe all multiboot partitions due to the way it is created. I can't comment about your backup, but I doubt it is a multiboot image backup. You'd probably be better of making a backup of your data (like our autoback does), flash the multiboot version of the image, and restore your data.
If you have OpenPLi (7.0-rc+) in a partition, you can flash the other partions from within the image.
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