In all of these post I did not see any mention of compacting the files before trying to merge them.
When ever you are doing major operations to FTM files, I would recommend that they be compacted and an error report ran on the file. (FTM Version 16 and before it is activated by a key combination, later version as a report in Publish.)
I would correct all major errors and re compact the file again before continuing to the merge operations.
I find that anytime I am doing major additions or editing to my FTM 2012 file I have less problems if I frequently compact the file. Making backup with each compacting in not a bad idea. The time it takes to compact and backup is less that the time and hassle that it takes to correct problems.