Source PDF documents that include PDF transparency groups are not rendered correctly when flattening them. The layers are converted to white backgrounds and are rendered as different objects.

This feature is not included in the product. If you need it, please submit a Request for Enhancement.

An alternative solution is:

1. In SmartDashboard, go to Threat Prevention tab.

2. In the left tree, click on Profiles.

3. Select the relevant profile - click on Edit... button on the toolbar.

4. In the left tree, click on Threat Extraction Settings.

5. At the bottom, in the File Types section, select Process specific file types - click on Configure... button.

6. In the pdf line, right-click on the Extraction Method column - select Clean (instead of Convert to PDF).

   Example:
   

7. Install the Threat Prevention policy.

This solution has been verified for the specific scenario, described by the combination of Product, Version and Symptoms. It may not work in other scenarios.