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If your Kindle is jailbreaked, you need to (temporarily) disable that jailbreak in order to install Amazon signed updates.
I doubt that this check result has any consequences. From its name I think it's clear that file isn't supposed to be there.
Besides that: How should we help you to revert the changes you have made when we do not know which changes you made? I'm sorry, but you will probably have to go this route alone... Better ask about specific problems you encounter.
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