Hi Jesse,
Stack aligner is only currently capable of aligning images by translating in x and y, so it can not correct for the rotation at meridian flip. However, since your images are plate solved, you do not need to align images to run multi-aperture, even with a meridian
flip. All you need to do is enable the Multi-Aperture option "Use RA/Dec to locate aperture positions". Then AIJ will first locate aperture positions by RA and Dec (rather than X and Y) and will then centroid (if enabled).
Actually, with AIJ 3.3.1 and later, all you need to do is plate solve the first image and the first image after the meridian flip (or the first image after a large jump in pointing if its not a meridian flip). In this mode of operation, "Use RA/Dec..." mode
places apertures by RA/Dec if an image is plate solved, and by X,Y coordinates of apertures in the previous image if not plate solved. To use this mixed mode of operation, the Multi-Aperture option "Halt processing on WCS or centroid error" must be DISabled.
Karen