When flattening a markup or image, the colors associated should remain the same. You can click on the "Revu" drop-down and select "Preferences". Then, you can select "Advanced" on the left side. Your "Rendering Engine" may be the issue, and if it's set to "Software", then this issue could occur. Another solution involves using the "Create" tool. It can be found by selecting the "File" drop-down and mousing-over "Create". Then, you can select "From File". This will allow you to create a copy of your PDF that "fixes" incompatibilities with certain markups and images from other programs. After doing this, you should be able to flatten anything without distorting their colors.
If you saved the file and closed it, there isn’t a way to unflatten the file. I recommend making a copy of a file before flattening and incorporating this into your workflow. If you still have the file open, you can press the “Undo” key and “manually unflatten” your data. If you must, you can also use the “Edit PDF Content” tools to remove the flattened data and re-create it with Markups and Measurement tools. Best of luck!
