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Are you sure you removed the modules with the red arrow in the control panel before you deleted the files?
My guess is you only deactivated the module by changing the green V in a red X. That means the module is still counted as installed in the database, it's only not active. After you removed the files (I guess) I can imagine the system does strange things.
If what I describe above is what you did I would try to re-upload the files in the module maps. Then remove the modules using the red arrow. After that you can safely remove the files.