Ttowntenor, you are understanding how Merge is
supposed to work.
"While merging, if a BookID is found that already exists in the Songs Database, the BookID stored in the KMA file being merged is renumbered to the lowest free BookID available."
I've not heard this problem before. Thus, my first inclination is to suggest your reinstall Hoster from scratch by doing a REMOVE then Installing again. I would use 3.321 as it is the latest release.
I'm interested to hear what you find after installing. If the problem persists, we would need to get 4 files from you; 2 pairs of duplicate BookID's to dissect and see what the Headers contain. That is the source of what we use in the Merge.