I'm using a MacBook Air that has the latest OS update. Prior to the update, I had no issues editing, merging, or combining files. Now, when I attempt to combine files, it gives me an unexpected error and does nothing.
Which version of Acrobat Pro do you have (e.g. Adobe Acrobat DC Pro, Adobe Acrobat XI Pro, ...)? When you say the latest OS upgrade, I assume you are running Mac OS X Sierra (10.12.x). I cannot find any information in the Acrobat XI/DC release notes in regards to Sierra, but this page here suggest that there should not be any issues with software that is currently supported: List of compatibility issues with Adobe Creative Cloud products running on macOS 10.12 (Sierra)...
You will run into problem with Acrobat X and older.