Sounds like the bed has gone to where it's very anaerobic. You do periodically need to clean a grow bed, particularly if you have a relatively heavy fish load for the amount of grow bed space.
It's important to prevent any of the solids and water from getting back to the fish tank if you can because there are toxic compounds like hydrogen sulfide, and methane present (both of these are gasses but will be released when you stir the sediment). These would likely kill the fish if you stirred them up and flushed them straight into the fish tank. There are a few videos on YouTube about cleaning AP grow beds (RobBob has one I know).
Having worms in the grow bed helps keep them aerated and it's possible if fish loads are light and everything is sized right, to go years between cleanings.
The plants may be salvageable if the roots aren't rotting. You may be able to just pull them, set them aside, clean the bed and then replace them (kind of depends on how big they are
). Pulling them will stir things up so proceed with caution as far as the fish are concerned.