Were these changes done as markups with the Commenting tools? If they are, then you can export the markup from the 2nd and 3rd versions you could choose Comments > Export Comments to Data File. This would export FDF files which contain only the comments. Then on the 1st (the master, if you will), you can choose Comments > Import Comments, and import the FDF files from the other two, uniting the three in happy matrimony!
Yes, all the changes were done with the Commenting tools. Sorry, I'm probably not explaining myself very well--I don't want to merge the three drafts into one .pdf, I need them to remain separate entities in that I need a process flow .pdf, a field verification .pdf, and a SIP/CIP .pdf (all of the same master). I just want to be able to make an alteration to the master and have it automatically update the slaves.
(A similar thing exists in SolidWorks, for example. The .prt file that is the 3D model of a part or system is "mated" to the .drw file that is the technical drawing of the part. If you change, say, a dimension in either the .prt or .drw file, the dimension will automatically update in the sister file.)
Sorry, I'm fairly new to Acrobat so I don't know all of its capabilities yet.