Capturing Cortex Vs Reference

So I’ve been having some success capturing. I have some come out great and some come out so so.

Tonight I was capturing an amp with an overdrive in the chain. When the capture was done I’d do the reference / Cortex back and forth to hear it.

I began to think since I have the pedal engaged the reference should sound like what I wanted to capture. The Cortex should sound over the top since it’s a capture with the pedal and the pedal is engaged.

Well that’s not the case, engaged them both sound the same , disengaged they both sound the same.

Made a capture without any pedal and did a reference / Cortex test ( my bud gave me the idea). I moved knobs on the amp while on Cortex and the tone changed!?! How can that be if that is the capture ?!

Anybody looked into this before?

Update. I went back to it and I wasn’t using any real reference meaning monitors.

No change with the captured tone when turning knobs.