Hi,
I assume your refer to the SDRAM tab in the Qsys component "Cyclone V/Arria V HPS" (or something similar). This tab allows you to specify the memory parameters for the External Memory Interface that the HPS connects to. In the HPS, there is a dedicated SDRAM controller and it needs to know the type, speed, calibration settings, that will be used when setting up this interface. Once you compile the design, the details in this tab will be used as part of the hardware-software handoff folder. Then, when you use the bsp-editor tool to create the preloader, information from this folder will be used so that the preloader will be able to calibrate this interface successfully.
If you are able to start the HPS successfully (and access the DDR3), I assume that your preloader has been loaded onto the SD Card/QSPI and you did not change/modify it. Thus, even if you recompile your design for the FPGA, as long as the preloader remains untouched, the HPS DDR3 calibration will still be successful