[Darryl Ramm]

It's still not perfectly clear what you are describing? If you have monitors connected to the Eleven Rack and you play guitar through the Eleven Rack and you hear output from the rack that is not controlled by the Pro Tools faders... that is just the Eleven Rack local hardware monitoring circuit that Pro Tools normally quietly disables. It has nothing to do with Pro Tools signal flow, except Pro Tools normally just magically disables it. That it is still working means you either don't have the Eleven Rack selected as Playback Engine, the driver is hung of faulty or is being upset by the microphone security settings in some strange way (that would surprise me).

An easy explanation here as well is that you let your mac sleep/suspend with the Eleven Rack connected in which case the driver will hang, it will show up in Playback Engine the MIDI and control parts may work, but audio will not get to or from Pro Tools ...that is expected behavior. You need to reboot the Mac. If you previously had done the systems optimization to avoid the mac sleeping/suspending, you may have lost them in the macOS upgrade.

If that is not it then uninstall and reinstall the latest Eleven Rack Driver, being careful you accept any security questions that appear (run the installer with no windows on your desktop that can hide pop-ups).

I head earlier misread the OS version as Mojave, but if you are on High Sierra, this won't apply: go into systems preferences > security & privacy and enable microphones for Pro Tools (Apple really means all audio inputs not actual microphones).