It will look like this:
Incorrect flattened
Correctly flattened
It is essential to flatten files with such transparencies. Here’s how you can do this:
In Illustrator
You can flatten transparencies directly by using the "Flatten Transparency" option under the Object menu.
In InDesign
Follow these steps:
Create a new preset via the menu Edit > Transparency Flattener Presets.
Choose the "High Resolution" setting, click "New," and name your preset.
Adjust the Raster/Vector Balance from 100% to 75%.
Check the box for Clip Complex Regions in the lower section.
Leave the other settings as they are and confirm by clicking OK.
Finally, export your design in InDesign as a PDF and choose the PDF/X-1a:2001 preset in the PDF menu. In the Advanced menu on the left, select the newly created flattener under Transparency Flattener Preset.