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calibre stores position marks for annotations and bookmarks in the epub unless you remove the checkmark from Keep a copy of annotations/bookmarks in the e-book file, for easy sharing (viewer => preferences => miscellaneous.
As far as I recall, the information is stored in the META-INF directory in the ePub zip container under the filename calibre_bookmarks.txt so deleting that file would remove those changes.
As for never altering source files? Which alternate universe have you been living in?
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