I’m using a AeroGarder as seed starter with my grow but I potted my mine. I transferred some herbs years ago. It involved cutting apart the plug cradle. Pulling the plants through, when I encountered tangled roots I cut in the middle to separate. Then cut most root ends and remove any knots and planted them in soil and watered to run off. I would have followed the same basic process if I was going to a larger aero\hydro setup.
It was by no means a “gentle” process. Those plants didn’t miss a beat. I don’t have firsthand experience doing this with marijuana. I suspect marijuana would have responded the same way, but that’s just a hunch.
What I did take away from that is don’t cross that bridge. You could use their seedling starter solution or copy it transplanting before it’s an issue or just start the seeds in soil and ditch the watering feature. The AeroGarden controller is nice and the LED panels are great for seedlings.
Good luck with your extraction.