Well, you should give the FTM's file merge utility a try before getting started. As I wrote earlier, I don't think it will work on a large scale, because it's just not up to snuff. It will work, however, on a smaller scale--when used in a piecemeal fashion--so if you understand how to use it, it will save you time. (I just recommend never allowing it to make any decisions for you, because I wouldn't trust it with my own data.) With 20k people, you need things that will save you time.
What I'm talking about is under the file menu. There is an option there to "Merge...". You should learn everything about how that works. Also, learn how to use the export feature as well, because that will save you time by allowing you (indirectly) to delete the people from the other tree that you've squared away in the destination/final tree.
Here are two things to note:
- File export allows you to create an extract of your tree based on what you select. This is the only automated way of (indirectly) deleting large groups of people from a tree. You delete simply by not including them in the exported tree. (You would want to do this after you've imported a group of people into the final tree.)
- File import allows you to import a single person or groups of people from another tree. You select what you import. This works well when they don't exist in the destination tree. Then you only have to establish the parent-child relationships to connect them into the destination tree. Otherwise, you have to deal with merging duplicate people and duplicate facts--and you have to compare the data with which you started with the data post-merge. Proceed with caution there, but don't be afraid to try it out. That's what backups are for.
You're probably going to be dealing with a lot of exports and backups as you're combining this data into a single tree. Back up methodically, frequently, and with notes!!! Make sure that you make a note somewhere of every family tree file you have, what you did to create it or modify it, etc. This project will take a long time to complete, so you'll need this process to be documented in case you ever have to back up because of a mistake you made. The final integrity of your data will be determined by how organized and disciplined you are, but it can be done. You're sacrificing a bit of time now for greater time savings and data in the future. That makes it worth the effort.