Custom Critters issue. Possible currupt file?

I'm right on the verge of publishing another arc and ran into an issue with custom critters. Basically I've been riding the edge of storage space and seemed to be at or around 95%. I had to remove minion mobs from my groups to get to this. I suddenly reallized my boss mob for my villain group was missing. I figured it's more important to have a boss on the villain group than ally group and both are similar looking so I simply moved the boss from ally to villain group.

Now I'm at 101%! But it was a lateral move!

I went into critter groups and found a duplicate and deleted it. Still at 101%. I went into the actual file folder and found another log for the boss, deteted that, still 101%. Basically it's counting the boss that no longer exists and I don't know how to fix this. I've scoured all my groups and looked at the file folder, to no avail.

I'll now be at 95% with no bosses which is worse than if I hadn't tried to move the boss in the first place. The only fix that I can think of is deleting the group and starting over but that will be huge and not sure if it will work. Any suggestions?

EDIT: After deleting the boss mob from one group, I found that my space was 90% with an error. Clicked on the error and one of my major characters from a group not even associated with the original problem is missing! WTH??

I abandoned changes, clicked on that character directly from the custom tab and ran through the edit just clicking next, next. Went back into arc, now it's at 95% with the mob showing but not attached to the objective. Reattached I'm at square one again. 95% and no bosses.

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I always have to do this kind of thing with direct file editing. There are multiple places where the MA editor stores critter and faction references, and it seems to restore them if any of them aren't trimmed.

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And for a while things were cold,
They were scared down in their holes
The forest that once was green
Was colored black by those killing machines