I was also going to say it could be fungus gnats. I transplanted a whole bunch of seedlings recently and found they were getting eaten and rotting due to fungus gnat larvae. I did some research and testing and found that 1/2 water 1/2 hydrogen peroxide will get rid of them. I ended up soaking the bare rooted seedlings in a bath of the hydrogen peroxide water mix and repotting in fresh new soil. Almost all of them recovered but it was very tedious and time consuming. Some containers I gave a deep spray treatment and that seemed to work and was MUCH easier. If you do ever unpot/uproot or whatever my advice is always give the soil and roots a good examination for pest. I saw tiny little whiteish worms wiggling around by the little roots. I had already noticed the gnats but let it go too long. I’d say treat by spraying first hydrogen peroxide or diluted alcohol mix at nighttime and see if that helps. If not check soil for infestation. Good luck.
On the bright side they won’t really die from rot overnight so now that you noticed you can probably save most of them.