emusonacid!

The scenario: I set up a cord to route MidiA to filter cutoff. I turn the knob on my controller to change the cutoff. Now when I disconnect my controller, the filter cutoff is stuck where I left it. It makes sense, but now I want to reset the modulation so I can hear the filter at its original position.

(for anyone asking why I'd disconnect the controller, that's not the actual scenario. The actual scenario is midi automation coming from my DAW. But same thing applies - once I stop my DAW, the modulations are all stuck where they were last put. Again it makes sense but I'd like to reset the modulations on the emu so everything is at its original position)

Use the function "Reset All Controllers" in your DAW.
This will send on all MIDI Outs of your MIDI-Interface and on all 16 MIDI-Channels of each MIDI Out the CC-message #121 that is defined in the MIDI Specification as "Reset All Controllers".

You can also create a "part" or whatever it is called in your DAW and create a CC-message (Bn 79 00) with the List-Editor.
"B" stands for the MIDI Control Change Command, "n" is the MIDI Channel 0-F (hexadecimal), "79" (=121 decimal) the respective Controller for the reset and "00" is a default value, needed to satisfy the requirements of a MIDI-Command that has to have a length of 3 bytes.

Your DAW likely will overwrite the MIDI-Channel in your created CC-message with the value set for this track.