The middle sticky approaches it from the side (in your case).
Calibre needs control of the files and can't guarantee that if the if they are at the mercy of other programs (or the user
Books Added or Removed must be don by Calibre to sychronise the DB with the files. Anything else will usually end a mess.
Tell your ComicRack to use the Calibre Library... It probably has the same problem.
Choose your poision... That is your best choice.