Regarding Renesas Synergy MCUs: I want to modify a header file which is automatically generated by Renesas's SSP. Does anyone know if there's a way to prevent SSP from overwriting these files?

First of all, SSP modifies every software generated file automatically and also updates those generated already. If it is a configuration related coding that you want to preserve, I am sure it can be done via SSP itself. If it is user code, you may position it within areas specified for the same.

A generic alternative may be you can create a separate header file, write your custom code and add the file to the workspace. In such a case, you may have to #include this header file in your main code.