Unfortunately not...
You don't have to reset them all – you can reset just the Keyboard Maestro Engine's Accessibility settings by running this command in the Terminal app:
tccutil reset Accessibility com.stairways.keyboardmaestro.engine
Have you run the Keyboard Maestro Editor's Interactive Help from its Help menu? If not I would start there.
I would probably rebuild the launch-services database with Onyx before resetting the KMEN's permissions.
KM should be checking for secure-input problems, but just for giggles I'd run this macro:
Macro: Find the App Responsible for a Secure Input Lockout - #8 by JMichaelTX