Yes, that's a possibility. That's why I asked in the first post in this thread whether or not your pressure gauge is rising. You indicated that when you backwash you're getting brown and green stuff washing out--is that still true, or is your backwash water clear? How does your water look at this point?
If your pressure gauge isn't rising, and you're no longer washing out brown/green stuff with your backwash, then I would suggest keeping the pump on recirculate until you're completely finished shocking the pool and it all is dead, and then shutting the pump off and letting it all settle to see if you can vac it out to waste.
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