If small enough, you can water them...then gently dig under them with a spoon, lift it out, and place in proper soil. Make sure to go all the way under the roots. I used to germinate a few seeds per cup, and transfer when needed. (had limited growroom space)
When placing in fresh soil, you can bury it up to the cotelydons. (the round 'baby leaves') This is something I do with every strain, every plant. More roots will soon grow from that stem, and it keeps the plant from stretching too much (and falling over) in veg.

If worried about digging them up, you can water them, pop them out of the cup or pot, gently 'massage' the old soil off of the rootball, then place in proper soil. If you don't break or crush, they will be fine.

Leaving them may create more problems down the line.

No nutes till the 3rd or 4th internode, 1/4 normal strength till they acclimate to the new food.