So, after posting I found two posts of this same issue, both approximately a year ago:
The first one from @WolfPai notes that on Windows, the preferences file that includes shortcuts is located at C:\Users\user_name\AppData\Local\BraveSoftware\Brave-Browser\User Data\Default\Preferences, and reverts to the defaults when brave is relaunched.
Like @WolfPai, I also have 2 instances of 39003 , the first one corresponds to what is displayed in the settings, while the second does not, and is always ["F10","Alt","Alt","AltGr"], regardless of what I set. Modifying the file manually does not change browser behaviour, and the file does automatically reset even without relaunching brave, but not every time I open it and check it, it’s on a 30 sec timer or so…