Yes, and ugh. That would have been a fine solution in 1994, but today there is no reason whatsoever to use legacy non-Unicode text encodings for languages like Hebrew. I've never used BibleWorks myself, but it's just like the stuff I face on a daily basis - many people who learned how to key non-Latin scripts in the 90s are reluctant to give up their legacy-encoding fonts, so after a few years of hassling my Lao and Cambodian translators, I just give in and write text conversion scripts for them (or custom keyboards that let them key in their preferred keyboard layout yet generate Unicode text).
I did a bit of digging around for you, and found that there are Word macros already written that will handle the BibleWorks -> Unicode conversion for you. I doubt that every single one of these steps will work for you, but in your shoes I'd
1) Export perfectly-styled text from InDesign to RTF (or go back and get that source Word doc)
2) Open RTF in Word
3) Use a Word macro to convert text from BibleWorks to Unicode (link to Youtube showing particulars including .exe download that is supposed to do the conversion for you)
4) Place RTF back into InDesign and clear overrides (or re-place Word doc and re-format)
If you work on the CC you can change your preferences in the CC app, right above in the corner is the gear symbol: Preferences > Language, there is one entry with English with Hebrew support for RTL texts.
If you are in an older version before CS6 you need to download a plugin with ME support or buy a ME version of InDesign.
Joel answered the rest.
Thank you for your input. I found that by tagging every word with the BWHebb font with "dcrit" (short for diacritics), I could then use the CSS selector @font-face to define the name of the font and the location of the font file (bwhebb_0.ttf), load the font in with my e-book, and then define .dcrit as font-family: bwhebb. No problem. I will certainly use a Unicode going forward to avoid this headache!
Thank you for your useful feedback. When you say "CC app", do you mean the Creative Cloud app? If not, what does CC stand for? Is this something built-in to InDesign CS6? If so, how do I access it? I'm trying to find information on the web about it, but I'm not certain I am understanding your acronym correctly.
Edit: Now that I have done some more research, I think you are asking if I work on my e-book conversions within the Creative Cloud app. My answer is no. We use ScribeNet for our conversions. I am looking at how to get right-to-left support within Adobe InDesign so that we can publish scholarly work on Hebrew and other Near Eastern ancient languages. What I have currently found that works as a solution is to simply use the left-to-right bwhebb font and then tag all occurrences with <dcrit></dcrit> so that I can point the selected words to an embedded font. It's clunky, but at least the text renders this way. In the future, I would adore being able to use a Unicode Hebrew font, but apparently what happens is Adobe flips any right-to-left text in Word around when importing the file! This means we have to go through and manually re-key every consonant and vowel point, which is extremely labor intensive and unacceptable.
We are currently working with ScribeNet to figure out a work around, but it sounds like this is a deficiency with Adobe, not with our conversion process. There are numerous languages in the world that are written right to left. Perhaps Adobe InDesign should take this into account?
Everyone who is subscribed to the Creative Cloud gets the Creative Cloud Application installed. Normally this app launches with computer start. When it is running you have first to login to use it. In the preferences settings in that application you can choose which language your programs should have. One selection can be, English with Hebrew support. If you do RTL projects you should use it. It will have no negative impact to your English projects.
Prior to the CC versions you would have to buy either a ME version from the programs or buy seperate plugins to get RTL support.
EPUB conversion can be done via export from InDesign. All EPUB functionality has been strenghtened with each version, even with each dot version.
I do not subscribe to the Creative Cloud, so that rules that out.
However, I see at this link: http://helpx.adobe.com/indesign/using/arabic-hebrew.html that I can accomplish right-to-left in InDesign CS6. However, I cannot locate the button they're talking about that lets me swap between left-to-right and right-to-left. I have the Paragraph options panel up, and I have selected "World-Ready Composer" from the drop down, but nothing seems to happen, and there certainly is not a button akin to the one in the image.
You need the Middle-Eastern version of InDesign for the extra right-to-left type/story features. Without it, you have to resort to right justification, I believe. At least, that is what I have been doing.
Adobe needs to fix the right-to-left importing of Hebrew when you place a document. It seems to work okay with not reversing the Hebrew letters, however, if you do the old "Copy and Paste routine. At least this is a workaround.