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After you flip it export it as a new image with no watermark applied. Then apply your watermark to a second export of that exported image.
Does the watermark now show correctly when printed?
The rotating of the image in LR doesn't change the original rotation. It only gets changed for displaying of the image. If you export it the rotation you made is burned in to that exported new image. Then applying a watermark on another export will place the watermark in the correct position and rotation, Not Flipped.
Thanks, this works, but needs to be fixed, the print module for the original file displays the watermark in the correct position, but doesn't print correctly. The extra export file, then add the watermark to print does correct the issue. Just takes a few extra steps.