Chrome prompting for custom protocol handlers every time after update
Are you using Chrome 77? Than you are not the only one with this problem. https://support.google.com/chrome/thread/14194567?hl=en
This is intended The "always open these types of links in the associated app" checkbox is missing because the devs discussed that it wasn't right as there is no option to undo such a choice. Can't make it better than that. Sorry, I'm just here to give you information.
So it looks like for now, you don't really have an option. They removed this option because once you click the checkbox "remember", you can't undo that choice. So they just deleted this feature (as the source link states).
I just found a way to re-enable the checkbox on Windows.
You can follow these steps:
Open regedit.exe as Administrator
Go to the key
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Policies\Google\Chrome
Open or add the dword name 'ExternalProtocolDialogShowAlwaysOpenCheckbox' and set it to 1.
Restart Chrome and test your custom protocol. It will show the checkbox again.
You CAN undo an allowed protocol, but you will need to edit the preferences file under your profile folder and search for "protocol_handler": There is currently no undo option in the Chrome GUI.