Did you try a search of the Bluebeam forums? Oh, wait, ........ never mind.
What I do for a set, is always split the drawings and rename the files by sheet number. (R-A321.pdf, R-A314.pdf, etc.) I do NOT save changes to the original architects file.
They will at least slip-sheet/supersede correctly. You can easily cut/paste markups from one page to the other.
The reason I do this is I have seen files named
"R-A321 - BRICK COLOR LOCATIONS. pdf" changed to
"R-A321-BRICK COLOR LOCATIONS.pdf" which screws things up.
This slight change in file name is easy to miss.