In my retro rig I did a 100 % hardware DOS6+Win3 / Win95 dual boot, where they can not possibly even see each other, and therefore will never interfere with each other.

This was done by adding a physical 2-position rotary switch to the front panel. Then I put two IDE-CF adapters inside to same cable on Primary channel, and set jumpers on both to Master. The power cable wires are split to go directly to both adapters, except for the black wire, which goes through the rotary switch. Now when ever I switch it to either side, it only powers one adapter but not the other.

When I switch to one it only sees the DOS FAT16 drives, and when I switch to the other it only sees the Win 95 FAT32 drive. Works perfectly if one wishes the operating systems to be 100 % invisible to each other.

Last, put on stickers so you remember which is which, and a big warning label to never use switch when power is on, because there is zero chance of anything useful happening. Haven’t tested that, and probably shouldn’t.

I use a StarTech CF to IDE adapter and two industrial grade CF cards for this purpose.

The StarTech adapter mounts in one of the 3.5" bays on the front of the case. This allows me to swap CF cards at will, and requires no more effort than inserting a floppy disk. Of course, the PC needs to be turned off while changing CF cards.