Just a shot...
I guess I'd next check how you've set up the skin. In the Skin Editor on the General tab, you've got Index selected right? Also, on the HTML Help Setup tab, how have you set up the Index Options (a separate window off the Skin Editor)? For my imported-from-RH projects, I've got Binary selected but not Include bookmarks with index entries. (I'm telling you this purely FYI.) If you play around with those settings, does that have any effect on your output?
If the skin looks OK, can you confirm whether or not there are any index entries in any of your topics? If you discover that there are no index entries in the topics, then I don't know what do suggest. I think you're out of luck. I don't know of any way, post import, for Flare to separately process a RoboHelp HHK file.
The last ditch thing I would try, assuming there are no index entries in your topics, is to create a new, separate Flare project and re-import the original RH project, trying different import options to see if you can finally yield a set of Flare files that include the index entries. Then, with both your working Flare project and the temp Flare project open (you can launch separate instances of Flare), copy and paste the index entries from topics in the temp project to the corresponding topics in the working project. I completely understand that this will be painful, but it's the only other solution I can think of.