I changed my miners from a modded large number 5 drill to an extra large number 5 drill and when I try to change the main entities it says "Cannot reduce size of module inventory". It won't even let me go back to the regular drill which only has 3 module slots instead of the eight that my number 5 normal drill has.

You can work around this by making a blueprint with the drill you want in.

You can export the current blueprint and change the drill, before updating the blueprint and reading it back in.

It is to avoid the possibility of trying to put more modules in a miner than will fit, though the check should probably be skipped if you're not using modules.