It does not scan the contents (aka read metadata) of anything other than ebook files. And MTP is a transacted protocol you can pull the plug on it anytime without corrupting anything, in any case what calibre is doing is read only to all but the calibre.driveinfo and metadata.calibre files so nothing on your device can possibly get corrupted from it other than those two files which you can delete and have calibre rebuild anytime you like..
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