Multiple altitude drops, EKF3 lane switches/primary changes

Hello devs and fellow pilots,
I built a custom folding hexarotor. I recently reached out to the forum for help earlier, but I believe I have a new issue.
Hardware appears to be working great in Stabilize flight mode. We performed an auto tune and it flies very well. We often get a “Compass Variance” error in the HUD, but we’re not sure that’s related to this issue.

While in AUTO, and sometimes in LOITER, the drone will randomly drop 2-3m quickly, and then regain altitude at a reasonable rate. It hasn’t caused any crashes yet. But we do not want to put a camera on the platform until it can perform missions with no issues. (Drops in altitude would ruin our photogrammetry data anyhow).

Any ideas on what would cause this? You can trace the altitude drops and see multiple “EKF PRIMARY CHANGED” messages at each drop.
I’ve attached a link to the .bin file. Thanks a million!