Are you copying from Illy to ID? I recommend Place-ing the Illy file instead. If you must copynpaste, make sure Illy is set to AICB instead of PDF, just to see if that helps the dotted line thing.
You do know that you can edit any Preflight profile in order to make it do (or not do) what you want it to do? Click into the Panel Menu Button of the upper right corner of the Preflight Panel, and you can get in and edit the profile.
Thank you for the response.
Place-ing files limits the errors to 1 per diagram. The books generally have anywhere from 350 to 700 diagrams, so that would take a bit of work to separate them all into individual files. But at the end of the project, it would reduce the 3,000+ errors down to 350–700. So that's definitely more manageable.
Copy-and-paste would be simpler, but unfortunately the AICB setting did not solve the dotted line issue. But I was unable to select the "Preserve path" option even with AICB selected. It could be a bug with the recent 2015.03 release. It looks like the radio boxes are interfering with the Cancel and OK boxes. I'll keep an eye out for fixes.
Regarding the Preflight options, the publishers/printers definitely want to keep the 1pt rule for complex colors. But from an aesthetic standpoint, 1pt lines way too heavy for the origami diagrams. So I was hoping there would be an option to ignore this rule only in instances where the lines are made up of the specified red or blue 2-color mixes.
Thanks again. It's very much appreciated!