thanks for using our tool. I think the problem comes from original image files being moved (or deleted from the hard drive by the user). It is true that the yf5m file embeds original images (to avoid the path issues mentioned before), but it only does so when images belong to a panel or a figure. However, images are not embedded (they are instead directly read from the drive) when they are removed from a panel and sent back to the original list. In the latter case, if the original image file does not exist anymore or if its path has been changed, then the image is simply deleted from the original list. I did choose this for various reasons when I coded the tool, but maybe this was a wrong choice, I’ll see if I can think of a quick workaround or if I think of a code fix to avoid these issues and I’ll do my best to keep you posted in a few days.
@imagejan thanks for letting me know, I would have missed this post without your help.