I assume it's the sudo halt. Ongoing write procedures may be halted at once too. That can corrupt your SD card.
Better use is sudo shutdown -h that waits ongoing write jobs are finished.
As you noticed, there are two mount points boot and rootfs, the second would be the one with all the good stuff on it.
Under ~/.octoprint is the bulk of what you'd want to backup. Run my command from earlier that begins with cat (the conCATenate command is good for showing the contents of a text file). That command I gave you will simply report the plugins you added to the installation (from the octoprint.log file).
The file named just octoprint.log is the latest. Anything with a date decorating the end of that is progressively older, in archive terms, depending upon the date you see in the filename.
Halt is in my opinion, using .NIX OS's for almost 30 years. Halt is "hokey" it stops the services, but not the underlying kernel. And SD cards are not the best "hard drives" Yes buy the "uber" version, but they all get hosed. SanDisk has a WinTel tool, that kind of works. Personally I use GParted. It is a multi platform tool. Yes, you hose the drive, put a new partition on it, format it the way you need it. In our case fat32. But 128gb sd cards use a different format type so windows can find it. ext32 I believe. Gparted doesn't have that format type. I can refresh a 128, using fat32 with relative success. Your results may vary!
I think I'd go with: "Use Etcher to flash the microSD with the IMG file of your choice whether that be the OctoPi image or the Raspbian Stretch Lite image".
The act of formatting a microSD leads to more problems than you can imagine (when there are actually two partitions of different types on a standard Raspbian hard drive).