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I came here today specifically for this problem (merged books into wrong target).
[in book list mode]
I had a bunch of book entries that I merged together. In all cases (since I sorted the list by title) as it happened, the ones I wanted to Keep was the Second title.
ie:
Book1 dup
Book1 Master
Book2 dup
Book2 Master
Book3 dup
Book3 Master
So I would click on the second title, and then use cursor keys to ALSO include the first title in the selection. Then merge them.
In every case it ended up that the First Title became the target/master instead of the Second title.
This happened to about 6 books before I noticed what was happening. So I reverse sorted the list by titles so that the entries I wanted to keep were the first in the list and finished merging the books without problems.
Since I know that I have in the past used Mouse clicks to select books to merger (when they were Not next to each other in the list) and it worked as I wanted, I suspect that because I was using the cursor key (up arrow) to include the dup entry in the selection that this was the cause of the failure, and maybe what caused other people to have the same problem.
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