As a former critic and still a historian of the theater, I call a show that had a long run and made money a "hit," a show that had a short run and lost money a "flop," and a show that had a respectable run but lost money a "show that had a respectable run but lost money."
There is also, of course, a category of shows that had quite short runs but still made money and were thus hits, because, for example, they opened in 1906 (like Forty-Five Minutes From Broadway), or played a star-driven, SRO limited engagement in 2006.
The terms "hit" and "flop" do not necessarily correlate in any way to the length of the run. Still less do they correlate to the quality of the show--Broadway history is awash with masterpiece flops and also with hits that were absolutely dreadful. They only refer to financial success or failure.
If you like the term "masterpiece flop," you're welcome to it, or any other mitigating adjective you like.