I want to add lines on canvas prints to mark the edges for wrapping

I create gallery wrap canvas prints by cloning the edges of the image - to be used to wrap around the stretcher bars.  I use Perfect Resize to create the cloned images.  The cloned parts are saved as layers. In Photoshop I add some canvas around the image and use the line tool to make marks on the outer edges at the layer edges -  and those will show me where to put the stretcher bars.   

I have been doing this for years - but lately I cannot keep the lines when I flatten the image or when I send it to my printer.  I used to flatten the image and the lines would reamin.  Now they disappear ... Did the line tool change???