Image Processing and Analysis

I don't really use QuPath, I don't like it. But the person before me used it to annotate images and now I need to transfer these ROIs/Annotations to ImageJ where my pipeline is. Managed to find a good script for exporting with annotations, but it seems this person transformed the images (differently each time fml), and I need them to be the right orientation because I'm transferring those annotations to another set of images of the same samples from another microscope. Needless to say, I need to do some image registration, a very easy task /s. So is there any way to at least revert back to the initial orientation before export so I make the registration easier? I'm using SIFT which isn't really capable of accounting for mirroring/flipping, so that step really needs to be fixed beforehand. Any ideas? Or at the very least, is there a way to extract transformation history from the Metadata or so such that I can at least use that info to programmatically revert in ImageJ?