So she followed your instructions and got dual boot by accident, instead of by plan.
ME is the last OS where you can actually talk to the hardware.
The various INT’s work as they do in DOS mode.
How do you know she has ME? I ran two Windows 2000 installs on the same partition with no problems, allowing me to boot into either directory.
Just restore your system and get rid of these directories. You said you have a backup. Now use it.