Thanks for the heads up Allen. Some random thoughts...
No issues here with my IC40/ipH setup. I posted a concern for this very scenario when I was first considering an ipH. I was told by someone here that I did not have to worry about messing up my pool should that ever happen, as dumping the entire contents of the tank into the pool would not greatly impact my plaster. The pool would quickly recover, the water would rebalance, and so not to worry. Further, as per Pentair ipH instructions, I dilute my 31% acid 1:1 with water, which means there's never more than about 1.5 gallons of acid in the tank at any given point. Not enough to be much of a concern should the system malfunction. So I quit worrying about this.
My setup needs the main pump to be on about 8 hours a day in order to dispense enough chlorine and acid and solar heat, so even if my pump schedule malfunctioned, it would have to run for days to empty the ipH tank, and I'd hear that, so that's another non-concern for me. Your main pump schedule is something to check, for sure, but even if it was running for days non-stop, I doubt that alone would empty an ipH.
If wired correctly, the ipH can't pump while the filter pump is off, just as the IC40 can't produce. And the ipH doesn't dispense while the IC40 is producing, the ipH controller turns off the IC40 just before it dispenses. It's the ipH controller that runs the show to make all that happen, which leads me to believe there was a malfunction in the ipH controller, because the ipH is not controlled in any way by the EasyTouch (except for main power). The EasyTouch does not schedule or initiate the acid dispensing. Did they replace your ipH controller? I'd expect that to occur if this happened to me. I'm not sure why they replaced the pump. The acid pump gets its power from the ipH controller, so I don't see how a malfunctioning acid pump could empty the tank unless the controller was also malfunctioning.
For what it's worth, my current IC40 is running fine with the "no salt" issue. Pentair replaced my faulty IC40 with a new model, but I never installed it (and they never asked for the faulty one back). I figured that as long as the "broken" one was making chlorine, I'd run it until it dies, and have the replacement as a backup for when it does. Point being, the well-known "no salt" fault doesn't appear to affect the operation of the IC40 or the ipH. So I don't imagine that replacing the IC40 switch would resolve this issue. In fact, I recall some here with the "no salt" problem replaced their switches and that didn't resolve the "no salt" problem. I don't think we ever collectively figured out exactly what causes that issue, but I don't think that has anything to do with your acid tank issue. The ipH controller monitors the IC40 flow switch, and won't dispense without flow (or isn't supposed to). Maybe the switch was reporting flow when there was none? That sounds like a long shot. That still doesn't explain why the tank emptied, as even if the flow was 24/7, the ipH controller is only supposed to dispense a little at a time. Sounds like your warranty guy is shooting in the dark.
Regarding the "new" pump... I can't say if there is a third pump. Pentair should know, call their tech support and ask (though that would be a somewhat obscure question for them, so they may or may not actually have the answer). Is there a part number you can see? If that number matches the older style pump, then that would at least tell you if you have an old one or not. I would not be the least surprised to learn a local pool repair company used some part that they've had stuffed in the back of the shop for years. (Which is how I ended up with a pool light that only lasted a few months, as I was sold an old one that didn't have the newer copper heat sync.) Pool guys... sheesh.
I would follow up on this until you're assured you have the newer pump, as the older one was replaced for a reason (though I can't now recall what that reason is). Ride Pentair and the repairman until you get the newest pump and a new ipH controller. Chalk this up as a fluke, and keep an eye on the ipH moving forward. Checking the tank contents should be a daily chore, along with spot checking the filter gauge, the leaf baskets, the water level, etc. The problem with automation is that it will eventually fail, so you need to treat every day as the day it might happen...
Even if this was a known issue (which it is not, as far as I know), I wouldn't stop using my ipH. It's way to convenient.