Configuration Persist is required in Tandem PROM configuration. Dual purpose I/O used for first and second stage configuration cannot be re-purposed as user I/O after second stage configuration is complete.
If you attempt to reuse these dual purpose configuration I/Os or use the STARTUPE2/E3 primitive you will see an error similar to the following:
Do not remove the BITSTREAM.CONFIG.PERSIST from the constraints set, but do ensure it is set to the appropriate configuration mode (for example, BPI16).
If the programming flash device must be updated after initial programming, external connections (not via the FPGA) are required.
Configuration Persist is not required for Tandem PCIe, as the second stage bitstream is loaded over the PCIe link.
To use Tandem PCIe in UltraScale, enable the following two options to turn off PERSIST and write two separate stage1 and stage 2 bitstreams.
set_property HD.OVERRIDE_PERSIST FALSE [current_design]
set_property HD.TANDEM_BITSTREAMS Separate [current_design]
Note: The above properties are for UltraScale devices only.
More information can be found in PG054, PG023, and PG156.