What do you mean when you say “…the lenses for both cameras were swapped to a longer focal length and recalibrated.”
Specifically what do you mean by “recalibrated”? Are you re-calibrating the intrinsics for the cameras (which are now different because of the different lenses) and then calibrating the relative pose? Are you calibrating the rig with stereoCalibrate() and having it compute everything (new intrinsics for both cameras and relative pose) If so is your input calibration data sufficient to do this (enough 3D points, not all coplanar etc)? Are you assuming the intrisics didn’t change?
I’m not an expert on 3D vision, but my understanding is that in order to get true measurements of depth you have to have fully calibrated cameras (intrinsics & relative pose). With less calibrated setups (unknown intrinsics) you can get depth measurements up to an unknown scale (so relative depths “point A is twice as far away as point B” but no sense of units), and / or up to an unknown projection (where relative scale isn’t necessarily preserved, so you can only get things like “A is further away than B”, but not “A is twice as far away as B”). If these concepts aren’t familiar to you (calibration up to an unknown scale / unknown projection) it might be helpful to read up on this.
Again I’m not an expert and I might have described some things wrong here, but the sense I get is that you are trying to get actual depth measurements but don’t have a fully-calibrated rig. I believe what you want/need is to calibrate the intrisics for both cameras of the stereo rig (independently) after putting the new lenses on. Use calibrateCamera() and a calibration target (I prefer the charuco pattern). After you have calibrated intrinsics calibrate your rig and use this full calibration in your process…you should be able to get the same depth measurements from both rigs, but with different depth accuracy.
This web-based calculator might be helpful in giving insight into the accuracy (and FOV etc) you can expect from different lens (and baseline, sensor resolution etc) choices: