SDC file for clk from Native Phy

Sorry that it was a bit late on the reply,

In Timing anaylizer we can set multiple clock frequencies if you have a switch outside the FPGA. https://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/manual/mnl_timequest_cookbook.pdf page 7.

However, since yours is related to dynamic reconfig of an PLL, What you can do is look into the example design https://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/an/an661.pdf download the pll_reconfig_mnc.qar see how they constrain the sdc. If there are nothing inside, means they expect customer to test it on their hardware to make sure it works.