The most critical aspect of Nested DFX is the additional importance of bitstream management. Not only must all full and partial bitstreams be generated from the same design version (using a consistent locked static image), but lower-level partial bitstreams must have consistent locked logic above them. pr_verify is used to confirm this consistency prior to bitstream generation, then users must manage bitstreams appropriately once they have been created. Tools such as the DFX Bitstream Monitor IP can be used to track bitstream versions during device operation.
Moreover, lower level partial bitstreams must be delivered only when their RP is active in the design. It is the responsibility of the system designer to build their controller solution such that it permits appropriate delivery of a lower-level partial bitstream. Nothing in the silicon will natively stop an incorrect partial bitstream from programming the device - as long as the Device ID is correct, the configuration engine will let it in.