I can confirm that using latest RetroPie in latest Raspbian Stretch with stable EmulationStation it does recognise files >2GB as @mitu stated:
Created a test "rom":
$ dd if=/dev/zero of=$HOME/RetroPie/roms/psx/test.pbp bs=1M count=3072
Then restarted ES, the rom appears and ES tries to launch it normally. Of course the emulator returns immediately, but it IS recognised by ES:
lvl2: EmulationStation - v2.7.6rp, built Jul 11 2018 - 17:57:30
...
lvl2: Attempting to launch game...
lvl2: /opt/retropie/supplementary/runcommand/runcommand.sh 0 _SYS_ psx /home/pi/RetroPie/roms/psx/test.pbp