dgallup,
So far, the OP has logged in once.
I worked in a place where they had the SolidWorks files controlled by SolidWorks PDM, and a second document system which controlled PDFs and STPs, which were used for manufacturing. If you needed to modify something, you checked the files out of the PDM system, you made the changes and checked them back in. Once you and the other designers were happy, you filled in an ECO to replace the stuff in the purchasing database.
If this were my system, the primary form would be an ECR (Engineering Change Request). Its primary job would be to describe the problem. Attaching a red[‑]lined drawing would be optional. An ECR committee would work out if the problem was serious enough to be worth fixing. If so, a qualified designer would work out the solution, and they may or may not follow the red[‑]line.
In another company I worked at, with aggressively process[‑]driven people, the red[‑]line would be implemented by a CAD monkey, quite possibly demonstrating the problem you describe, above.
I claim that we do not understand the OP's question. He may be askng about a custom software application that may or may not allow red[‑]lined PDF attachments. He (or she?) may be dealing with an in[‑]house ECO process that may or may not be well designed. Do they have an ECR system as I describe, above? Is the ECO generated by someone with a problem? Is it generated by a committee that is responding to someone with a problem? We don't know.
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JHG