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