Having decided to convert everything to more modern substrate instead of plain old dirt from the forest, I was looking at some of the trees this weekend. The November rains have started up, so everything is soaked and a couple of the pots have very soggy dirt. That should lead to root rot according to just about everybody who knows, so I am wondering if it would be a good idea to repot into proper substrate now or let them sit (and possibly rot) until March or February.

Opinions?

Don't repot now, unless you have a very good idea what you are doing. Better protect the pot from too much rain..

You probably know, but roots do not rot from water per se. It is the lack of oxygen which may cause parts of roots to die, and then they may rot.

If they are in bonsai pots, tilting the pots also helps with drainage.