Updated images are showing fine inside Animate, but when viewing the published output, old images are shown instead of the updated ones. Looking inside the images folder, I can see that old images are actually being published so not a browser cache issue as originally thought. Deleting the folder and publishing again did nothing.
Other things I've tried is to copy all layers and frames into a new file, switching publish settings between Texture, Spritesheet and Image Assets, and even reinstalled Animate, but still nothing. Another different project that uses some of the updated images has no issues with publishing so I don't think it's an issue with the images themselves.
One thing I haven't tried though is deleting the images from the project and reimporting them as there's over 100 of them to be fixed and I'm hoping that there's a simple solution that I overlooked.