Flyers2020's post in Random Win10 Agents Corrupt was marked as the answer
received a kb article from support.
running the elevated command restores the endpoint agent config file:
"c:\program files\malwarebytes endpoint agent\configurationrecoverytool.exe" "c:\program files\malwarebytes endpoint agent\mbcloudea.exe"
would be even better to restore remotely/manually instead of interrupting users to touch their PC's.