Daka no Oni said:
Wait, if you add more maps, do the bosses just not work in the new maps, or do they just not work period?
They don't work at all.
Well, Balrog, Igor, and misery work. The rest don't.
If you delete maps and add new ones, the glitch still occurs.
This only happens with Sue's Workshop.
However, if you don't plan to go beyond the 95 maps already in Cave Story, this can be worked around by editing the maps that already exist into entirely new ones, rather than removing them and adding new ones. They can be resized in properties.
If you wish to rename a map, or change the sprite sheets it uses, that
must be done in Miza or balfrog, frenzied toroko, monster x, the core, ironhead, the sisters, the red demon, the doctor, undead core, and ballos will not work. They will simply cease to exist in your mod if you modify map properties.