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My friends and I have started to grow bonsai from seedlings together, and as such I have a young mugo seedling.

It was doing rather well and strong, but I noticed today that it was flopped over onto its soil and wouldn't hold itself up. There was water gathered in the bottom of catch tray, so I know it's been sitting in that and resultingly drowning. I've just moved it into shade and exchanged some wet soil for dry soil around the roots. The base of the plant seems pale and somewhat damaged.

Is there a potential it will recover? Is there anything I can do to aid this process?

Where have you placed your seedling? If its inside it will die
A picture would help grately.
Btw you do know that there will not grow a bonsai out of these seeds but a normal full grown tree?