Character style suddenly not working

This document includes Arabic characters and many Roman alphabet italic characters with diacritical marks. I created character styles for the latter and spent hours selecting each character and applying the style. It was perfect. Now I've opened the document again and all the character styles are lost. If I reapply they don't work maybe once or twice, and then they don't.  Using Roman rather than Times New Roman Italic for these diacritical characters seems to work, but it won't work for bold small caps characters (it did before).

I am NOT basing anything on the dreaded "Basic Paragraph." In fact this happened after I changed all my styles so they are not based on it. 

If I redefine the character style by hand it makes no difference. If I individually style each character it makes no difference.

Since I can't delete preferences by holding down the keys (it just doesn't happen) I have uninstalled and reinstalled the program. The problem persists.

Attached are a PDF showing the correct fonts and the document. 

Was my mistake moving the same styles from another document into this one?