LC makes my stack a substack

[stam]

I've only skimmed the above, but agree with others:
the substack may still be there and causing issues as the go stack command presumably sees that first.

To make sure, you can look in the Project Browser (Tools menu), navigate to your mainstack and see if the substack is still there.
Or even simpler, just type in the msgBox:

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put the substacks of stack <your mainStack>

Regardless, if you want to specifically access a stack (even if named same as a substack) and assuming you have saved your mainstack, you can just

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go stack (specialfFolderpath("resources") & "/" & <stackname>.livecode)

and not rely on implicit paths - be explicit...