I'm creating a DVD menu in Hindi. I don't speak Hindi so someone had created the menu in Hindi using InDesign; the idea being that I could just copy and paste the text into After Effects so I could animate the menu before exporting it to an m2v. However, when I copy and paste the Hindi text into After Effects the text becomes altered. It looks right but when compared to the text I just copied from InDesign it looks slightly different. I've overcome a similar problem when creating an animated DVD menu in Arabic using an After Effects script from the site below.
Could you export the text as a PDF from InDesign, then either import it directly into After Effects or open it in Photoshop to manipulate it (maybe put each block of text on a different layer) then import this into AE? That way, you'd hopefully eliminate the risk of characters/accents being substituted during the process, which might happen if you copy and paste.
This is assuming you don't need to animate the text per-character.
It reminds me of a job I worked on many years ago where the Arabic artwork was supplied as A3 prints, with no indication which way was "up"! We just went with what looked about right, and got lucky!