Adding to the comment on point 3. We are now certain that the directions in our data before and after August 2021 were consistent.
The directions in the original opt12 scheme (given before the start of the scan, Philips calls this scheme in the rotated MPS frame) were in RAS format with reference to the image coordinate system. This is the same direction scheme we used for all our participants.
The directions in the Dicoms were in LPS format (Philips calls this LPH in the patient frame) with reference to the real/scanner/patient coordinate system (more accurately defined as the patient coordinate system because we were using FFS: Feet First Supine orientation). This explains why the directions in the dicoms between our participants were different, as each scan was angulated differently.
Our fsl bvecs converted by dcm2niix (default setting) and mrconvert (stride -1,2,3,4) were in LAS format with reference to the image. This explains why the x-axes of our fsl bvecs were flipped when compared to the directions in the opt12 scheme (RAS), and why the directions between our participants were the same.
All this to say that we have checked the orientation and flipping of axes in these various formats. They were all correctly transformed within a participant and were consistent between participants. Despite consistency in the bvecs and the image protocol between participants, we are still seeing incorrect orientation of tensors and tracts for scans done after August 2021.
For point 4: We posted a separate detailed summary of our investigation scan here: Inconsistent primary eigenvector orientation in differently angulated scans of the same subject