Earlier I wrote that turning on NPAPI plugin support to Chrome is a kind of task for "power users". I have found some instructions how to do it and perhaps it is not that bad. If using Java is still critical, you can give your users short and clear instructions. Which ones?
Since the date of Java shutdown in Chrome is approaching, I would like to write a review of Java uploader vs. its HTML5 counterpart. What features you will lose if you switch from Java to HTML5? Are they critical? Let's try to figure out.