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To make Process Hacker "stealth" , you need to create a file ProcessHacker.exe.settings.xml in the main program folder. Otherwise it'll save settings in appdata.

This information is not mentioned in the program page. I came to know about this on visiting their website.

It is mentioned in the program page. A quote from extraction instructions:

Create an empty text file named ProcessHacker.exe.settings.xml in the x86 subfolder for 32-bit or x64 for 64-bit