Ralph, re the large merge you mentioned. You are right in that normally I would never expect it to turn out well. In this case I had a 17000 person tree into which I merged a 3500 person tree, however only 500 persons or less were one and the same. And even those 500 were identical in data, media and records in both trees. So FTM had no apparent challenge as there weren't even data alternatives to be considered.
To make a long story, the two trees were subsets of a 40,000 person tree I have that won't sync anymore with its Ancestry.com counterpart. Nor will it even upload/sync as a new Ancestry tree without FTM crashing. Support has not been able to identify the problem. The backup I had has the same problem and the few database correction suggestions e.g compacting to 0 after closing the tree does nothing, and I can't use Publish without crashing the tree. I can't even export large branches without FTM crashing. What I have to do is create a new tree with one person, then merge into it the individuals selected from the 40,000 person FTM tree. That's what I did and since both of the resulting trees came from the same data source, they were not a real challenge to merge into each other.
Enough rambling, Hope you have success with your problem.