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Also of note is that the timer does still go down before you meet the Lunatic, and if I recall the default config has it set for only 7 days or so? So if you're slow to start and don't change the config, it can absolutely screw you over way early. Of course since I dunno how long you spent, it could be whatever.
That said I think if you remove the mod, your world will be restored to perfectly working order, so then you don't have to worry about that and can continue.