I have an Arria 10 with HPS on board. When changing the clock frequency of the h2f_user0_clk in Platform Designer from 100 MHz to 125 MHz, nothing happens. Measuring the clock shows me that it is still 100 MHz. I read in the documentation that this is a software managed clock.
When there is a change in the Platform designer, it should be recompiled and the bootloader should be regenerated as well. The HPS settings in the Platform designer are reflected in the handoff files and the handoff folder is the input to the bootloader generation process. You may refer to the flow in https://rocketboards.org/foswiki/Documentation/A10GSRDGeneratingUBootAndUBootDeviceTree