Try it with a card reader. The updater & Companion software should start up and you should then be able to merge. You don't need to have the DR1000 connected to the Computer.
The only caveats are the pdf and its associated metadata file
must be in the same directory (which they should be unless you've tried moving the pdf elsewhere)
and the files structure is as iRex assumed, in other words your directories & files are created in the Documents folder, otherwise the Compnaion software will not be able to see the metadata.db file and hence merge. see
https://www.mobileread.com/forums/showthread.php?t=31328
and for
Senkrad Luna,
The companion software works on a MAC under parallels and I therfore assume it would work under Wine in a Linux environment. It is a very basic piece of software. If you can use Linux, Thomega (as Allovertheglobe suggests) has written a programme that will merge without the companion software but I have no idea how to compile it for the MAC & have given up on that for now as Ross has done a version for the MAC but it does create rather large files.