I've heard the story about the 12th level magic before. It's Forgotten Realms history, which makes it a part of D&D multiverse lore.
But...
It seems to me that one can accept those events happened in the multiverse without accept the particular terminologies used. For instance, if you were playing 3e, you could just say that those 10th and 11th level spells were just Epic Spells that they had decided to classify according to the familiar spell levels, and the 12th level spell was a unique thing (as it was presented).
In 5e, there are multiple ways of dealing with it that don't rely on accepting that magic objectively went above 9th level. You could say that 10+ level spells are actually just variant ways of casting wish that produce specific (rather than open) results at the cost of the extra hoops you have to jump through. (In an extremely high magic society, they used language that codified these various results and such as different spells of higher levels, even though mechanically it was "cast wish plus do this stuff".) Or you could say they are all unique things rather than something that follows the standard spellcasting rules.
Although I find the contradictory lore in D&D irritating, there is usually enough of it that with most things you can multiple ways of interpreting the reality behind the lore.
One of my stand-by approaches to lore changes that I don't care for (like the way 5e presents the origins of the Yugoloths or MToF presents a lot of elven stuff) is, "some people on some worlds believe that".