Factorissimo needs a looot of internal mod savedata for all its scripted stuff, and can't work without it.
Converting saves to scenarios strips all internal mod savedata. So Factorissimo2 (and also any other mod that uses internal mod savedata) will break once a save is converted to a scenario. The only way to avoid this is not to convert saves using such mods to scenarios.
Just continue playing on the savegame from before you converted it to a scenario, and try to see if there's a mod that can do ingame what you tried to do in the editor (for example Creative Mode).
