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You can easily keep multiple copies in calibre, but you need to consider the Calibre directory structure a closed black box, and don't put things in it, or take things out. Change things only in the Calibre GUI (or with the Calibre command line tools.)
If you just add the pdf to Calibre, it'll keep only one copy if you have any kind of duplicate detection turned on, but it won't automatically remove duplicates you added explicitly.
Easiest way:
1) Add one of your pdf's
2) Add an empty duplicate entry in Calibre (ctrl-shift-e, or click the dropdown beside the Add Books button and choose add empty entry. There is a "Duplicate this book" button at the bottom of the dialog.
3) Add the other pdf to that entry, either via the Add Metadata dialog (top right) or Shift A or again the Add Books button dropdown and choose "Add book to selected record"
And be careful if you use the find duplicates plugin, but if you do, you can mark them as exceptions so it won't keep suggesting you merge them.
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