The fonts should work in PDF format (I have the Sony PRS-505); I have stuff with both the vowel length marked by lines and the dots underneath (in one of my Intro to Sanskrit files, it is a text based PDF, not scanned) and it shows up with no problem on my reader; however, when you use reflow it might reflow a little wonky. Other kinds of embedded text, such as Greek, etc. work as well.
Hope that helps. If you are really concerned, you can send me the file and I can try it out on my reader and upload a picture.
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