Naturally, when the mod isn't active it can't do stuff. Prototypes are created/modified during startup, in the data stage – the time before you get the main menu. If you have a saved game with things made by a mod, then restart Factorio without that mod, it can't create its prototypes or make any changes to existing prototypes – and the game will discard anything it cannot identify on loading that save.
The dummy that you have seen removed is created by this mod. It's used to store your inventory when you switch characters or enter god/editor mode. Basically, switching your appearance means that inventory contents and properties of your current character will be copied to the dummy, then your old character will be deleted and a new character entity (based on another prototype) will be created in its place, and everything will be copied back from the dummy to the new character.
If you restart the game and remove the mod that provided your last character, you can switch to a new character and everything will be restored from the backup. But if you remove miniMAXIme, the dummy characters are removed as well (plus, even if they'd still exist, the code to restore inventories/properties would also be gone), so you may end up without a character and lose all the stuff from its inventories, it's logistic slots etc.
Solution: Enable miniMAXIme again, load your last saved game, switch to the default character, and save. Disable miniMAXIme and restart Factorio. On loading your save, you should have a character again.
