Merging database's between Genealogy Programs and other fun

I purchased a copy of Family Tree Maker 2012 shortly after it was released and imported my current database into GEDCOM from Family Tree Builder.    Working with a fresh copy on Family Tree Maker I went to work to see what hints might be available for my tree.

At the time I also decided to start the trial so I was able to test drive updating the hints online and syncing it back down to my computer with Family Tree Maker 2012. Fast forward to a few days ago (right before the release of the 1940 census) to be exact.    

I was planning to start making new updates with Family Tree Maker but during the time between the release of FTM 2012 and this week I have been updating Family Tree Builder, and Family Tree Maker on an uneven schedule to say the least.  When I took the time to look at it FTM had 2449 names in the database, and FTB had 2339. 

I initially opened up FTM 2012 after doing some research and decided to merge a GEDCOM from the FTB database into my FTM database.  This did not go well as it left with a lot of duplicates and now my database was at 2800.  It created over 400 duplicates, which could have been based on my merge settings, but it was taking forever to get back to square one.    I even tried the reverse and created a GEDCOM from FTM and merged into FTB.  Family Tree Builder lets you see the duplicates but does nothing to get rid of them.

So far I was not heading in a good direction, because I still had another issue to contend.  I could see in Family Tree Builder what were the newest names in the database (based off REF ID), but I also have to go back and see what was the last time certain files were updated (concerned with post release of FTM). In FTB.  

On the other side in FTM I could setup a REF ID for each name, but I soon noticed that it was not in any specific order.  Newer names in the database were all over the place.  I don't even want to try and look to find last modified dates in FTM.  

I would like to keep both database's current but have not figured out the perfect plan to do this.  If anyone has any suggestions to make this as easy as possible that would be great.  In the mean time I am slowing verifying all information from FTB has been ported over to FTM 2012, which then I will create a new GEDCOM and import back to FTB as my new starting database for FTB.

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