I personally now prefer the larger stone's in place of the gravel type stuff....That way I don't have to worry about my GF getting anything stuck when I'm not around either.
I just recently removed all the smaller pebbles from my tank and left the big glass stone's in there, What I did was take a couple cup fulls out at a time (The water will get really cloudy) Then I waited for that to all settle back down and took some more out..etc etc..Until I was free and clear of the small stone's. Then I did a water change just to clear the water up a bit. It actually didn't take long for the water to clear. That should work for you also I would think.

If you wish to change them out.