Sdlog2 missing data; LPOS, optical flow, possibly more

I was flying my pixhawk v2 today running v1.4.1rc4 and EKF2 with, replay logging enabled, and sdlog2 priority set to medium. After my flights I opened the logs using px4tools and found that all the LPOS and FLOW data was missing from the flight logs.

Have any of you seen this problem before? How can I fix this?

I can send logs if that is helpful.

Hard to tell without seeing a log (can you share one?). Is your flow sensor working correctly?