How to refer to tag containing "-"

This is not possible. hashtagger follows the common hashtag syntax used by Twitter, Facebook and Google+. See FAQ Section. Use “12thPlanet” or “12th_Planet” as hashtag.

So what good does “regenerating” them do if you can’t recall previous tags with “-” in the permalink? I guess I’m failing to see how I can make my various tags work for this plugin.

As already mentioned the hashtag Syntax used in the Plugin follows a common syntax used on established platforms. I highliy recommend to use this standard also for your internal hashtags because then you are able to use the same hashtag also on these platforms. hashtagger will never support hashtags not following this common quasi standard. If you want to use hashtags best solution in my opinion would be to replace your existing tags to a hashtag capable syntax. You’ll find a number of Plugins which can do that for you, like e.g. https://www.ads-software.com/plugins/search-and-replace.