Here is something to think about when merging databases in FTM. If you have people in your databases with no birth or death locations, the system will not include these individuals in the list of possible duplicate individuals. If these individuals are in multiple trees, You will discover that you now have multiple copies of these individuals and no easy way to search the database for them. You will need to manually review your index and merge each set of duplicate individuals manually.
I had a few cemetery indexes that I had merged into several different trees. When I merged all my separate trees (over 20 of them) into a single tree, I discovered that I had multiple copies of the individuals from the cemetery indexes. The name, date of birth, date of death, and burial information was entered for each of these individuals. The records were 100% identical in each tree. The find duplicate individuals feature during both the merge and in the tools couldn't find any of these duplicates.
My emails to Tech Support for FTM have taken weeks to get a response, IF I get a response at all. I finally had to manually merge over 4,000 sets of duplicate records.