They convert into vanilla soils.

If it's a limitation of Dynamic Trees, and last I saw it was (from DT BOP), there are addons that fix it for themselves. Like Dynamic Trees Natura.

Is this with the most recent version, and on a tfc world?

You said DT-TFC uses its own rooty soil? If so I'm closing this.
If the issue persists I'll open it again, or you can if you notice it happen. Although it's not DT-TFC's fault natively. :p