Well, the codebase existed long before HTML5 was supported by pretty much any major browser (remember, HTML5 didn't really stabilize to the point an enterprise could use it until 2012). So you have to continue adding to it while you wait for HTML5, and its popular frameworks and libraries, to come to fruition. Oh, and we're an enterprise SaaS app, so all of our customers run on whatever version of IE was released 4 years ago.
If all your customers are enterprise and running from within that environment only, would they not be able to enforce a group policy where flash can only run for specific domain names?
Someone always signals there will be a price to pay. The thing is, the price is not high enough when compared to the profit you gain by continuing down the road you are on now.
Further to this, a lot of enterprise-type companies I've worked at who have web applications, but their primary business isn't tech, just don't seem to understand software maintanence, and as such won't put a budget towards it. Instead they'll just completely replace it X years later for Y times more than the maintenance would have cost.