Well, they're not supposed to disappear. I regulary run 20+ languages into and out of InDesign via RTF, and your Croatian text should be easy (compared to, say, Burmese). I copied your sample text into ID and exported an RTF with no character drops whatsoever.

Are you placing your Croatian text, or are you keying it directly into InDesign? If so, what kind of input method are you using?

What is the name of the font you are using in ID? Is it the same font you're using in Word/Pages?

In InDesign, select a single character with a diacritic (ž) with the text tool, then go to Type -> Glyphs. If you mouse over it, the popup should read "LATIN SMALL LETTER Z WITH CARON." If it's just a normal z, then something is wrong.

Do the same thing in Word - I don't know where they hide Insert Symbol on Word for Mac, but in Windows, the bottom of the Insert Symbol menu will report the Unicode name "LATIN SMALL LETTER Z WITH CARON" just as in InDesign.

my source text in ID was

čćžđšČĆŽĐŠ

and what I have got in epub and rtf was:

ËÊæπ»∆Æ–©

If you select capital-S-with-caron the text tool in ID, and then go to Type->Glyphs, the S-with-caron will be highlighted. If you mouse over it, the popup will tell you if InDesign thinks it's a S-with-caron, or a copyright symbol. If InDesign thinks it's a copyright symbol, then the problem is with your text. It's probably something like MacCentralEuropean, or some other of those 1990s-era OS 9 encodings. If InDesign reports it correctly... well, then I don't know what the problem is, but I suspect that it is not an InDesign problem. The fact that you have different problems when your text is marked w/Adobe Garamond Pro versus Arial Unicode is suspicious, but I suspect that you'll find that your Croatian text is encoded incorrectly.

Alternately, if you could post an example file (to Dropbox or YouSendIt or some other such service) I could analyze the file directly and tell you "It's a problem with the Croatian encoding" or "It works perfectly; something is wrong with your OS or your install of ID." By the way, please do tell us which OS you are using.

I opened your IDML file in CS5.5 - seems I haven't yet installed CS6 on my laptop. At any rate, I could export problem-free epub and rtf from your file. Yet the epub and rtf you posted on your Dropbox display the character drops. The fact that you can't even successfully copy and paste such text out of ID into TextEdit (and that I can) points to something wrong with your install of ID. I would expect that either resetting your preferences, or at worst reinstalling ID would resolve your export problems.