As noted in the F-Tile Dynamic Reconfiguration Suite Intel® FPGA IP User Guide, we recommend allowing the Intel® Quartus® Prime Software to choose reconfiguration profile IDs automatically. If the reconfiguration profile ID manual setting is still needed, add the assignment on a "per-IP" basis.
The assignment is on a “per IP” basis and not on a per-profile basis. An example of the assignment is shown below for an Ethernet MRIP instance:
set_instance_assignment -name IP_RECONFIG_ID 1 -to my_e25g_1_inst_1|eth_f_0
Assuming the design had (2) secondary profiles, then the Profile IDs would then be assigned as follows:
Base Profile ID = 1
Secondary Profile 1 ID = 2
Secondary Profile 2 ID = 3