I think this would be possible with command line, but how to do it with jTessBoxEditor as it would automatize a lot of workflow.
Since jTessBox supports multi page TIFF I think that might be the way, but how do I organize boxfiles in this case?
You will need to update the page number (6th column) in each box file and then concatenate the files into one. The page number is zero-based and needs to match the order of the individual pages in the multi-page TIFF image. Once done, you can verify by opening the image in jTessBoxEditor to check if the boxes match up with the image.