Hi @FanZhang,
ConfigTools requires a certain level of consistency to be able to generate the board configurations correctly, and changing the files that it generates would not allow that level of consistency. This is why it reverts any manual changes made in the .mex file when updating the code (even if it’s the only file that it’s actually being updated) in order to "keep the configuration synchronized with the project".

So not allowing the user to change the name of the generated files is a way of ensuring the configurations from the tool work correctly and seamlessly with the project’s code.
Regards,
Edwin.