Hello; When I must move crypts they often lose some leaves. The leaves and stems sort of dissolve. This can go on for a few weeks. The plants generally survive and start to have new growth. Can be a bit slow.
When I must move them, I try to scoop up a lot of gravel with my hand along with the roots. The roots of several plants can be intertwined. I then gently shake the plant while still in the water to let the gravel fall away. The roots can be very long and some of the longest and finest will likely break off, they survive this fairly well. I don't always separate individual plants and often replant them in a bunch to avoid further breaking of roots.
Sometimes only one or two main roots are attached and the plants do survive. If the main plant has sent out runners and the new offshoot has good roots, you can cut the runner and plant the new one on it's own.
When replanting I wrap the roots, which can be very long, around each other into a very loose ball and put that into a pre scooped hole. Then gently cover the roots while holding the plant in place.