I really don’t know, but it sounds more like a printer driver or printer problem, not specifically InDesign. Or, if you were using some special VDP software, perhaps the problem is there?

Here is one option:
https://creativepro.com/changing-layer-visibility-in-an-interactive-pdf.php

No, I don’t think there is a quicker way. You might be able to find a way to do it by exporting the text as InDesign Tagged Text, then editing the code in a text processor, or exporting the file as IDML and editing it in an XML processor, but my guess is that it would be very time-consuming just to figure out how to do it and there is no guarantee it would work. If you had thousands of entries, it might be worthwhile figuring that out, but if it’s just dozens of entries, it’s probably faster to do them one at a time.

Have you already created your index? That is, are you trying to change the index entries in a finished index, where the index is on the pages? Or you’re trying to change index entries that are in your body text?