hey Fractalicious, and thanks for the more info. sometimes i leave things in the cloner too long too, so i know how that goes. thing is, i put them in 1gal pots of soil and call it good.
first, i want to mention that i work at a shop that sells Under Current systems, and I get a lot of feedback on them. and both the shop owners use them; one crops a lb per plant while the other hasn't completed a grow in almost a year... there seems to be a lot that can go wrong with these, but when nothing catastrophic occurs then the yields are massive.
the guy with his stuff in order propagates with grodan cubes, and then moves the plants up to the 4 or 6 inch cubes before placing the rooted cube in the net pot, on a layer of hydroton (and fully surrounded/covered with the hydroton too). he drip feeds the top til the roots touch water and then stops drip feeding to encourage the plant to focus on rooting the water. also, he makes a big deal about not having the net pot sitting in the water. he says that his water level is about 1/2 to 1 inch below the bottom of the net pot.
if you were of the mind to move forward with these plants, i would think to try to get the roots thru the net pot and down into the water, and then drop the water level itself.
personally, i would take cuts as i describe above and start over as i see these plants getting rootbound if they are left like that, and that the time that they will take recovering will set you back even further vs starting new cuts in a manner that will allow them to avoid these issues in your system.
however you decide to go, i wish you luck!