So I believe the issue have been resolved. I just have to be careful as the previous version of Indesign did some default substitution and I need to adjust this manually, which is a bad news for me.
In which case, I have good news! When I face similar challenges - usually opening up very old Pagemaker or InDesign files full of Lao or Khmer or something along those lines - I like to use GREP Styles to apply appropriate complex-script fonts. You can do it with a normal GREP Find/Change query as well, but since I try to use paragraph styles, I find it faster and easier to do in the paragraph style. In fact, when I open up old files and fix the complex script stuff with a few style adjustments, I like to fire off an email to my retired coworker and say "Hey, remember when you made fun of me for wasting time on obsessive paragraph styling back in 2002? Well, I just updated eight thousand pages of legal documents, in twenty languages... took me ten minutes!"
So: if you have carefully groomed paragraph styles in your CS4 documents that are all set up with Benton Sans, you should make some character styles that only apply Winsoft Pro (or some other Arabic-supporting font of your choice). Then in the Paragraph Style, you can set up a GREP style that will apply that Character Style only to Arabic text or numbers, with the following query:
[\x{0600}-\x{06ff}|\x{0750}-\x{077f}|\x{fb50}-\x{fc3f}|\x{fe70}-\x{fefc}]+
Alternately, you can use the same query in the GREP tab of the Find/Change window, if you don't want to modify the paragraph styles. Those numbers in the curly brackets are Unicode values, so you can look up Unicode numbers for various types of character and exclude or include them in the search. This might require some fine-tuning on your part; Indic-Arabic numerals and punctuation are included, but I don't remember if parentheses and brackets and other such bidirectional punctuation are also included in this query. That said, it should significantly reduce your workload of manual font-wrangling. If you need help tweaking the query for your purposes, just come back to this thread and we can figure out what needs to be included or excluded.
When I change the font to any typical Arabic typeface, the Arabic text appears correctly., so it is now clear some substitution takes place in CS4, but I cannot figure out where it is set.
I don't think I was ever a user of Winsoft products - I much preferred World Tools Pro, as it gave me tools for handling CJK languages as well as RTL languages - but I do seem to recall from time spent in their time-limited demo that there was a setting buried somewhere that could change the default complex-script font. I also seem to recall a conversation with a designer in Lahore about how buying ScribeDOOR from Winsoft was helping her update old CS5ME documents, but sadly I don't recall any of the details.
Anyhow, best of luck, and don't hesitate to come back with more questions.
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