I found eugenias to normally be pretty hardy and can handle some rough handling. How were you removing the seedlings from the pot? If you are trying to remove individual seedlings from a community container, I think that is asking for trouble.
I normally allow the soil to dry out just a bit and then upend the container and carefully get the dirt/plants/roots out in one contained mass. I will then gently jiggle the soil and carefully disentangle the roots from each other. This allows for you to get as much of the roots, including any taproot, out of the container without too much or any damage. This is an all or none kind of process. After separating, I cover the roots with some soil while I'm getting the new containers ready. I always jiggle the container with the roots and soil to try and get as much coverage as possible. Then water the hell out of them. This usually works very well for me.
Indeed, it is a community container. And it's a big container (maybe 40cm deep), and the roots go all the way down (much bigger than the plants themselves), so it's hard to ensure that they come out whole. It's just a place where, whenever I have seeds that I've given up hope on, I dump them in there rather than throwing them in the trash. And sometimes I get lucky.
Clever idea, dumping all the soil out. It's a huge pot, but I don't mind getting soil all over my living room, it's just a concrete floor
Do you think potting into sand (with constant bottom watering) would be a good plan, to avoid the risk of rot from all of the water? Maybe a little biochar and clay for minerals while still keeping it inorganic - and then once they're established adding organic matter to the top of the soil? What about bagging and/or pruning to reduce water loss while the roots reestablish?
Thanks for the tips, everyone
Here's to hoping that I get a good survival rate!
ED: I went ahead and did it with the dumping out method, with a soil mix about 85% sand, 15% clay / charcoal. I've bagged them with the bags down to soil level, but open at the bottom, so probably ~90%-ish humidity (the last time I had the bag at leaf level and wide open, so probably only ~60-70% humidity). I did no pruning. So I guess now it's just keep the tray full of water and once or twice a day monitor to make sure that the soil is staying moist and that the leaves are neither drying out nor molding.