All 8 pre-filters were swapped out at End-Y AHU-1. Of the 2 Supply Fans, SF-1 was running. The 8 pre-filters on the other side (SF-2) where it wasn't pulling air were still in great condition and left alone. 
Also, all 8 pre-filters were swapped out at End-X AHU-1. Same situation as E-Y. AHU-2 side was not swapped out. The pre-filters still looked near brand new.
Another note worth mentioning is that of the 16 pre-filters that were replaced, the filtration level of each was MERV-12 or MERV-11. They were replaced with 16 new pre-filters that are all MERV-11. This will likely slightly increase the air volume flowing through the unit.