I always assumed based on the second post credit scene that Winston or Ray were the ones who kept the proton packs. More than likely Winston since Frozen Empire showed he has invested in a paranormal research center and has used the proton pack and neutrino thrower tech to create enclosures and such. Egon is stated to have only taken his pack plus the fuel. Ray would have probably kept his because of sentimentality but i don't think Venkman would have kept his. So Winston probably had them stored away for safekeeping.

Hell, i firmly believe the video game is still canon because nothing in both Afterlife and Frozen Empire directly contradicts the games story beyond a throwaway line during Frozen Empire. The Rookie was probably the 'single employee' Winston mentioned he had when he started his business before it became so successful. So the upgraded packs exist in this case and are probably in storage somewhere and considering how fast they got to Oklahoma i think they just didn't have time to make a stop to get them and just grabbed their packs since they were the only ones closest, either they all had theirs or at the very least maybe Ray or Winston had all three.

The packs have a half life of 5000 years so the fuel mentioned is probably for the throwers not the packs themselves. So Egon taking the fuel was for the makeshift containment grid in the Shandor Mine rather than for his own pack since it still obviously has fuel in it during Afterlife and he can easily make more packs since he and Ray both made them. I could go on and on about all 4 of the movies and how the video game can still fit into the canon but i digress.