I use System Commander on my retro computer to make it was to have multiple operating systems on the same computer.
It works pretty well until I accidentally overwrite the MBR record so that it doesn't start anymore and none of the portions are bootable on their own because system Commander messes with the partition table to hide one operating system from another.
I guess I have to hack myself again
And find something better than "fdisk /mbr" to add MBRs to compact flash cards
So I have successfully hacked my own computer.
It seems system Commander just sets the high byte to 1 to hide a partition. So I just changed 1C to 0C and now I can access the windows 98 partition again
Still can't boot though and the system Commander checkmbr program doesn't want to work
Progress though
I used a hard drive dock and an IDE to SATA adapter to change the partition type. That part worked great.
It's nice to use breaking things as an excuse to buy tools that you have been thinking about getting
Plus side of this, in testing the HDD dock I found the source for a program I've been looking for. I had a picture of it on my website but didn't know where the actual code was.
Downside is the CD drive on that computer seems to have stopped working. I was using it the other day, so that's odd.
I'm hoping I just bumped something when I was messing with the hard drive
Otherwise I might have to learn how to service a CD drive
CD drive does indeed seem to not be working. It kind of spins but the light doesn't blink and DOS gives me the abort, retry, fail? Prompt.
Which is annoying because I think I need to reinstall windows 98 on this machine.
I don't know why it won't boot so I don't know what to investigate and it sounds like I should be able to just reinstall over the existing install and not lose any data.
So I will need to order some new CD drives after I get back.
Okay, Okay, I fixed it.
It was a classic case of the solution not working in a way similar to how other things don't work so you ignore it and go try something else
The solution is to use the SCIN utility and select the "Enable System Commander" option.
The problem is that SCIN runs at a resolution of 720x400 67Hz and my normal monitor doesn't like it and shows an "out of range" error
The double problem is that the SVGA drivers for Windows 3.1 that I am using also do that when trying to run full screen DOS programs. I can run most DOS programs in a window so I'm not worried about it. It seems like a common thing and not a monitor specific thing so it trained me to think that the "Out of Range" error means the program is outputting something bad and not just that the monitor I am using doesn't like it.
Today I tried a different monitor and it just worked.
Windows NT 4.0 is still upset for some reason and the CD drive is definitely not working but the OS/2, Windows 3.11 and Windows 98 SE are working again
So that's nice
@PurpleJillybeans I also use CF cards but I like the "permanence" of the boot manager
Annoyingly it was trying to set up a CF card that got me in trouble and it was a thing that I already knew was dangerous and could cause issues
Teaches me to leave things as "good enough"
I also think I lost the restore disk image as part of updating my floppy emulator
Kyle Brown 
PurpleJillybeans 
tahosa