Correct on both counts.
If you delete them from both locations and run a Steam file integrity check, it will place a copy of them in the root game folder.
Then, at the first subsequent execution of the sim it will place a copy of the files in the game's root into the documents 1c sub-folder. This is the instance of the files being edited whenever you make changes to your settings, the ones in the documents sub-folder.
Actually this is exactly the process we Euros had to follow to update our .ini files when they were redone in a newer layout some time back in May, preceded by saving a copy of our control settings first (options->controls->save as).
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