Thanks for that additional info. I’m still unsure exactly what you’re doing but generally if you are rooting in water then you are ok to leave the clones in there while replenishing fresh water (and fresh O2) every few days until you see roots drop (7-14 days after cut)
If you are following a traditional/regular cloning technique - e.g., take cuts, add beneficials or rooting hormones, root directly into cubes, rock wool, soil, etc., then you don’t soak the clone stems for that long of time (2 days you said right now?). When I used to use rooting hormone I would let them sit for 15-30 min.
I would take those cuts, cut off anything that looks soggy, and then move them into rooting plugs right away.
Hope this helps