Once the image is flattened, it's flattened, so there's nothing you can do the the existing PDF to change that.
Do they show in a new PDF exported from ID using a setting that supports transparency, like PDF/X-4?
Thanks for your reply,
Unfortunately, it's too much work grabbing all the archived jobs, re-linking them then re-exporting all the PDFs.
But I've just found a workaround by exporting images from Acrobat, then re-importing into the InDesign layouts.
BTW, these boxes/lines don't appear in Acrobat, only when placed into InDesign.
When you place items in InDesign the preview is a JPEG proxy of the image or page, so it's very likely that the stitch lines are visible in the low res proxy but would not print. If it were more than a problem with the proxy the lines would have also appeared in the exported images.