Unfortunately, it isn't always obvious from the data which of your interpretations is correct. Take the following two fictional cases:
Case 1: The Limburger Gambit was popular for a few decades, but then grandmasters started playing the Limburger Gambit Deferred instead, so it fell out of fashion, although it is still a perfectly good opening.
Case 2: The Limburger Gambit was popular for a few decades, but then a response was found that refuted the whole line. It was played in one famous game, after which everybody abandoned it.
As far as the data set is concerned, the difference between these two cases is a single game, so it's not going to show up in the stats.
This is true, but I think there are many more case 2s where rather than an entire line being refuted in a single blow, gradually one side was able to find antidotes and the line stopped being a good practical choice. The Vienna is an example. So while it isn't always obvious, I'm hoping enough fall between your two Limburgers to be interesting.
The two biggest examples I can think of of "opening fell out of fashion but then was brought back at the highest levels" are Kasparov reviving the Scotch in the 1990s and Kramnik reviving the Berlin variation of the Ruy Lopez in his world title match with Kasparov in 2000.
Case 1: The Limburger Gambit was popular for a few decades, but then grandmasters started playing the Limburger Gambit Deferred instead, so it fell out of fashion, although it is still a perfectly good opening.
Case 2: The Limburger Gambit was popular for a few decades, but then a response was found that refuted the whole line. It was played in one famous game, after which everybody abandoned it.
As far as the data set is concerned, the difference between these two cases is a single game, so it's not going to show up in the stats.