I made an Indesign document (RGB).
I've placed an AI document (RGB).
When I export to an interactive pdf file, some colors changed and transparency doesn't work.
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The first thing that comes to mind when seeing faulty renders like this is that the source is mixing spot swatches with transparency effects. There are two effective ways to mitigate these problems. First, either convert your spot swatches to process, or set InDesign's Ink Manager to convert all spots to process. You can access the Ink Manager from the Swatches and Separations Preview pallets' submenus. Second, export as PDF/X. I've had good success with PDF/Xa:2001, but different RIPs may fair better with newer formats. It flattens everything with transparency effects. You may see some hairline seams on screen with a PDF/X, but that is usually just an on-screen artifact of how the file has been flattened. The PDF/X format is also a good canary in the coal mine, in that if you see a major problem on-screen (aside from hairlines), it will likely show up on the print.