Normally, the tools check that there are no driver conflicts during synthesis and shut down all drivers when start the configuration. Yet, one and the same line can be driven by different drivers in different designs. And, no logic is shut down in dynamic reconfiguration. I see that it is possible therefore that the new driver is connected to line before the old one is released. This is a short! How do they detect and avoid this? Hardly, user can do this.
Xilinx seems unable to answer that question
and their active reconfiguration does not work.