Well, I did a vertical mirror based on the advice above, but for some reason when I save the file and re-open it, there's a new file with an _thumbnail suffix appended. When I tried running BPP with the newly saved files, it blew up, I believe because of the thumbnails, which incidentally don't show up as separate files.
I got this:
Calibrating target frame 1 of 28
[2018-08-21 21:31:30] Loading target frame:
[2018-08-21 21:31:30] /Volumes/Astronomy Pix/Pictures/Astronomy/ZWO_Flats/Flats-0001 copy.fit
[2018-08-21 21:31:30] * Subimage 1 of 2
[2018-08-21 21:31:30] Reading FITS image: 16-bit integers, 1 channel(s), 5496x3672 pixels: done
[2018-08-21 21:31:31] 46 FITS keywords extracted.
[2018-08-21 21:31:31] * Subimage 2 of 2
[2018-08-21 21:31:31] Reading FITS image: 8-bit integers, 1 channel(s), 400x267 pixels: done
[2018-08-21 21:31:31] *** Error: Incompatible image geometry