First of all, welcome to Mycotopia!
Second, mushrooms will grow wherever light permeates, so this means they'll grow anywhere in your clear grow-bag. they might not push up to the top, but they're still fine. You may have to pull the substrate out of the bag to get to them. This is ok.
Maybe you can pull the substrate out of the bag to harvest and put it back in? Even if it falls apart, you could dunk it and put it back in the bag for a second flush.
Hope this helps.
