Deleting partitions shouldn’t mess up anything, unless the partition was still in use by something else.
So if you have a disk that is just used for Nobora, deleting all the disks partitions will not mess up anything. If you have multiboot from the same disk then yes, you have to be a bit careful to not mess up whatever you want to not delete.
But as I said this is just to make extra sure. First try just installing Bazzite over Nobora, it should probably delete everything. If not, then you can delete partitions and reinstall again.