Original color on scans

I have multiple documents I scanned using the Adobe Scan app.  The app "auto-colors" the scans and I have to go into format and change to "original color".  Half of my scans successfully converted to the original color.  The rest will not convert.  Yes, I have the "apply to all pages" turned on.  The original pages are off-white, but are coming out white.  Yellow and pink post-it notes on the pages are coming out white and will not convert to original color.  What happened?  How do I fix this without having to rescan hundreds of papers??  I need the original color!