I am working on a project where I have several images with the same name (IMG_XXXX.JPG), where the cameras are divided into different groups by flight date. I have found that if I export markers (Tools/Export/Export Markers), delete them, and re-import them, then marker coordinates are not reliably assigned to the correct image - in other words, the marker coordinates saved on one image don't reliably come back to that image, and are instead sometimes applied to another image with the same name, in a different image group. This results in all hell breaking loose during model optimization, and some very funky results when updating too.
Initially I thought I had made some badly-formed XML when I was importing marker locations from another project, but when I got the markers correct in the new project, then saved the project, exported markers, deleted markers, and imported them again, the problem re-occurred - green control point flags showed up on images in different groups, but with the same name, as images that were originally tagged with GCP locations.
EDIT - This is becoming more of an issue as I expand the project to cover 10 000 images +. pair selection time is dramatically increased if I don't remove GCPs, but if I manually remove them and re-add them by exporting, then importing markers, then I have to go through all the markers by hand and remove erroneous ones.