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This sounds like:
1) a permissions issue, or
2) the missing format isn't really there.
The merge code has three options. In one, nothing is deleted, and in the other two, you should always get all of the formats in all of the selected records. The format list is provided by other code in Calibre, and that list of formats is used in several places, so if the list of formats was wonky, I think you'd see other wonky behavior.
I'd look closely at the records before attempting to merge. I'd also run a database integrity check. Finally, I'd see if I could reproduce this failure on a copy of the records (made using ALT-M safe merge).
I can't think of anything in the merge code that could be broken this way.
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