What scan settings to use so that "Replace Document Colors" will work?

Thank you for the response and sorry that it's taken me so long to follow up. For now, I'm going to table the issue to gather more information and do some more testing. I will then re-post and include some examples.

There's another issue I've noticed that's related, but seems to be more of an issue with Windows. As stated, I use a high-contrast mode. I was using Excel 2010 and used the "Save as PDF". That worked fine and displayed as expected on my PC, but when I sent it to someone was it was "unreadable". I still have to find out what this means, but it's usually something like white text over a white background. When I switched my computer back to a regular color theme and created the PDF, the other user whom I send the PDF to could read it just fine.

I'm using the latest CC Acrobat version. Somehow, it's all tied into this high-contrast Windows 10 theme. Like other applications, the UI elements display correctly with inverted colors. But as far as the document goes, it depends on the program. Office documents like Word and Excel will invert the colors. But Photoshop does not alter the images. It seems like Acrobat works a little in both ways. It doesn't alter the document unless specified in the preferences, but scanned documents are treated more like images (unless there are scan settings that should be applied for scanning.