Help Please? Possible root rot?

Hey guys i have been in the process of moving this past week and had left my plants at my girlfriends house for safe keeping. it seems as if sombody had left the lid off my home made low pressure aero/bubble ponics system and all the reserviors water was in the bottom of my tent. The plants had probably gone 1 or 2 days with little water in the bottom of the tank, and the spray not working due to such a low water level. After cleaning up that mess and re filling my reservior halfway with ph'd water and a little botainicare pro grow and liquid karma, the plants seemed to spring back up a bit. its been maybe 5 days since the big spill and the bottom stems on all of my plants are dying and falling off. one of them is looking worse than the others, and looks as it it has even started budding early. Im not sure what i should do? I dont have pictures of the roots yet but it also seems as if they are very stained by the nutrients or starting to rot, they dont stink much though, just smells planty. They were doing sooo well!

that one may not make it back. it looks like it didnt like the nutes also.

Nute burn on top of no water.... Ugg

That sucks! I've asked before if trimming the roots is ok in veg and was told that it was ok in veg but not in flower. Maybe gently, delicately remove the dead stuff.... I'm new so maybe seek reassurance on this before you do it though Sorry that happened.

Root pruning is ok in veg and can promote new root growth!
but like knuck said not in bloom.

How would i go about trimming back my roots? i dont want to mess anything up, im thinking about transplanting the best (middle) plant into its own bucket as a mother, and cloning out the really tall one, and then trashing the one that is probably dying. any suggestions? how do i go about cloning? do i do it before or after i start flowering. My plants are exactly 60 days old today, i planned on flowering soon but i dont want to waiste time and money.

Well your plants are no where near ready for bloom! As for triming roots you just take a sizzors ant
trim them back to good looking roots! Similiar to cuting dead or frayed hair off.

other than the one plant that is dying why would my plants not be ready to bloom? the two good ones are both over a foot tall and are 60 days old. I thought 3 months was the time is takes for them to mature from seeds?

Well they just dont look ready i.e health of plant being the #1 thing i see.
not trying to harp mygrow just your yields will be affected. Not saying you
cant bloom now.

recovery time.

ok that makes sense. thank you guys a ton. the last thing i guess i am curious about is cloning. i think i have decided to just scrap these plants into a bunch of clones and start over from there. should i wait a bit and let them get healthy again before i do that or just start cloning once i get the superthrive and rooting gel? I just got a hps light also in addition to my dual switch LED. What light would be best on the clones/veg and what should once i start to flower?

Cloning is no different! Sick plants will produce sick clones, just get these back to health and then make clones
or bloom them