I had the following fixes, which opened the needed application in Chrome without confirmation each time. They worked well until the update of Version 84.0.4147.89 (Official Build) (64-bit).
Fix 1:
In C:\Users\<username>\AppData\Local\Google\Chrome\User Data\Default\Preferences
"protocol_handler":{"excluded_schemes":{"neededApp":false}}
Fix 2:
In Regedit: HKEY_CURRENT_USER\Software\Policies\Google\Chrome
Create DWORD ExternalProtocolDialogShowAlwaysOpenCheckbox =1
Any idea what changed or how to fix that issue for the new version? It doesn't happen with all apps.