PDF's will not go away, Flash will hopefully soon though. Like some other Adobe software, it will just be updated for security issues every month. It's so regular in fact, that I change my A/C filter every time an Adobe Flash/Acrobat security release is pushed.
Actually, I would think only database stuff would be in danger. JHAP, I would bet a dollar that's what it was. We ran into the same issues, and it was a bear. The disadvantage to PDF's is size, but with storage prices as cheap as they are, it shouldn't be an issue any more.
I played golf one day with a programmer that ran an entire factory off a floppy disk back in the day. Every bit and bite mattered then. Now, bandwidth usage matters most.
