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No, I'd just like to be able to change the logo when you reboot or your phone is in recovery.

@OP, I would think deleting the repo won't affect installed apps. However, I'll await Applejuiced confirmation.

That is correct, removing a repo wont effect an installed package.
And about the boot logo unfortunatelly it cannot be changed with a cydia app.
You can accomplish that with the latest pwnagetool. It has custom boot and restore logo support.
 
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