Processing photographs gathered by two flight missions

I am processing photographs taken with same drone and camera during two different flight missions (flying heights and overlaps are different as well as the strips orientation which are perpendicular). Assuming the the software is able to process these two sets of photographs my question is: which photographs will be used to produce the orthoimage?

Two different flights of the same mission plan? They should all be considered equal, but exposure and color changes will cause some lost matches. If you’re not using GCP’s then it could be a mess if a quarter has passed and the satellites have shifted. I would suggest at least post-processing all the photos together to equalize before uploading.