Schmalle

The OP wanted to change the programs (modes) on their Whammy pedal via MIDI which requires MIDI PC (program change) messages. This can be done via Command Center.

Go with 1/4" Out -> GI100 -> FOH to block the board's phantom power.

Slight correction to @rd2rk's list: Global Settings -> Footswitches -> FS3 = TAP/TUNER In Command Center set a FS to SNAPSHOT. The DEFAULT settings cycle 1-2-3-1-2-3. In CommandCenter set a FS to LOOPER. Use Bypass Assign for the 1 SwitchLooper. (otherwise you can only use partial functions of the Looper)

Ok. I figured out what threw me off so much. There is an autocalibration algorithm for the Expression Ins that has three steps: open circuit ( 3.25 V ) short circuit ( 0 V ) max. voltage / resistance (e.g. 1.62 V / 10k Ohm) If there is no expression pedal connected (open circuit / more than 3 V are read) the recalibration is triggered. A voltage source can trigger this by providing more than 3 V, too. The next step is to provide the min resistance / voltage (0 Ohm -> 0 V are read). The last step is to provide the max resistance / voltage ( the standard max resistance is 10k Ohm -> 1.62 V are read). If the last step is omitted a max resistance of ~2.3k Ohm / ~0.62 V is the default. It is indeed a voltage divider with an inbuild 10k Ohm resistance in series with the expression pedal. You can calibrate the Expression In to any control voltage in the range of ~0.62...3 V. My multimeter isn't calibrated so values can be a bit off. Correct me if there is anything wrong about this.

I know that you can control it with voltage in the range of 0..3 V. But I couldn't get it to work reliably and accurately with my lab power supply. I couldn't just plug in, apply 2.7 V and assume that the read value is 90%. This brought me to the conclusion that there is more stuff going on other than plain voltage reading. If you can get it to go, good for you. Let me know what you did, I'm interested.

Probably a "not enough power" issue with the power supply. If the HX Stomp doesn't get enough current for a split second that can result in a crash or a reboot. The HX Stomp draws about 900 mA at 9V. Your power supply therefore should at least provide 1000 mA (= 1 A).

Again, check your levels to make sure you're not trying to fix something that you can avoid with a proper gain staging. To exclude Helix from your signal chain but still be able to use your pedals you need an additional switcher with three or more fx loops: Loop 1: Helix IN -> Send 1 Loop 2: pedals Loop 3: Helix Return 1 -> 1/4" Out If you just engage Loop 2 you exclude Helix. If you use Loop 1, 2 and 3 you have the Helix setup like you have now. You wouldn't even need to change your Helix patch.

Before answering your actual question this might help: To get the most equal experience compared to plugging directly into the pedals it is important to match signal levels, because pedals can sound different with different input levels. Same goes for amps. If you don't use the guitar pad: Make sure that Global Settings -> Ins/Outs -> Send/Return 1/2 are set to Instrument and you use stock settings on the FX loop blocks. Make sure that Global Settings -> Ins/Outs -> 1/4" Output is set to Instrument and the big volume knob is cranked. If you use the guitar pad (you have a loud guitar, probably with active pickups that clips the input): Make sure that Global Settings -> Ins/Outs -> Send/Return 1/2 are set to Line and you use stock settings on the FX loop blocks. Make sure that Global Settings -> Ins/Outs -> 1/4" Output is set to Line and the big volume knob is cranked. In the input block (first block in the signal path) there is a Guitar Z option that you can set to 1 MOhm and listen if it changes things (Auto can change the input impedance if you use certain drive pedals first in the path). Have fun!

Test your mental model of the circuit by applying a control voltage and see if you get reliable and accurate results.

I don't know the sampling rate but it feels immediate and smooth. The expression input isn't measuring a direct voltage signal (like an audio signal) but the connected resistance between 0 and 10 kOhm (0 ... 100%). To achieve your goal you'd need some kind of controlable resistor. Something like this example of a digital 10 kOhm potentiometer. That specific electronic component can be controlled with an Arduino, Raspberry Pi or any other microcontroller that supports SPI.

Some expression pedals like the Mission Engineering SP1-L6H have toe switch. It allows you to switch stuff by applying pressure on the toe down position. You can use that to toggle between Wah and Vol. EDIT IMPORTANT NOTE: For the HX Effects you would need to modify the SP1-L6H and replace the momentary switch with a latching switch.

Helix HX? Doesn't matter whether you mean HX Stomp, Helix Floor, Helix LT or HX Effects - the answer is yes, you'd insert your pedals one of the fx loops.

The XLR L Out is probably defective: open a support ticket.

Weird. Both XLR outs (L and R) should behave the same - there shouldn't be a difference in noise depending of which of them you use. But they should also behave the same regardless of what input you plug into. A potential issue: The Helix outputs automatically sum to mono if using only the left (mono) output. This is true for both the 1/4" and XLR outputs. This could be an issue if your patch has the right stereo channel phase flipped. It would result in almost no signal when using the left channel only (L and R would cancel each other out when summed) which would appear noisier if you compensate for volume after Helix.

I got reasonably close with: Modulation->Legacy->Frequency Shift 212 Hz, Mode Up, Mix 50%

I always recommend the Behringer HD400 / Pyle PHE300. It's a cheap and easy to use ground loop breaker that solved my hum issues countless times.

The first thing that I noticed is that the fx loop block isn't deactivated when the preamp is on. This means you have two cascaded preamps which would explain the hiss. Also note that Helix's preamps are pretty low in level. Use the preamp's Ch Vol and/or the Output block's Level to compensate.

While that solves the DSP problem it also adds some new ones (noise, latency, complexity, MIDI).

If you could post your 4CM patch that would help. What amp do you use?

Post / attach a patch where this occurs.

For a pristine clean sound I have great results using the Del Sol bass amp (dirt cheap DSP-wise) with a guitar cab e.g. the 4x10 US Super. Start with Gain 10, Bright on, Countour on, Master 10 and zero out the eq bands. I tend to end up adding a little 1kHz and take away a little at 2kHz. If you want inbuild compression the Busy One Ch2 is another good low DSP clean amp choice.

The offset function decides which string offset is currently active based on the frequency. For example, if a frequency of around 110 Hz is measured, Offset String 5 will take effect because 110 Hz corresponds to the note A and the A string is the fifth string in standard tuning. With flageaulet tones the tuner will choose the wrong offset. For example, the harmonic on the A string's 12th fret vibrates at 220 Hz and is therefore closest to the frequency of the B string (246.9 Hz, second string in standard tuning) - Offset String 2 is active in that case.

I did a test with a frequency generator (440 Hz sine wave) and my Stomp's tuner is spot on. Is your reference not 440 Hz?

Two DSPs but four paths: Path 1A, Path 1B, Path 2A, Path 2B. Read the manual for page 20 [Serial vs. Parallel Routing] onwards.

Not really. Another HX Effects or an HX Stomp could do that via MIDI CC / Clock but that is probably overkill for you.