After running the AutoFlow file on the CCH ProSystem fx Scan SaaS site, the PDF I downloaded was not marked up.
When the AutoFlow file is downloaded from the SaaS Scan web site, if Run is selected instead of Save, the PDF will not be created since AutoFlow was launched from Temporary Internet Files. The PDF copy of the job from the web site will not have AutoFlow markups as it was created separately from the AutoFlow process.
Always save the AutoFlow file before running the AutoFlow Wizard. The PDF with markups will be created in the same folder to which the AutoFlow file was saved.