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?
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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.