I prefer to choose just one time line from one possible ending as the theme of the sequel.

As for spoiling the ending of previous game, that can't be avoided so give spoiler alert.

OR

create the sequel using different character which doesn't spoil that ending in the first minutes of gameplay.

Another option is to take a side character from the first game and tell their story.

I've played game series (Mass Effect for example) where you could load a save from the previous game into the new one, so it knew exactly what choices you had made. Another approach I have seen is having an NPC at the start of the new game ask the player what happened to them before. The player then selects dialogue options to explain the route they took in the previous game.

It very, very heavily depends on the game and the story. And what people call multiple endings. And how much illusion of choice was involved.

Some of those games that boast multiple endings do not really have multiple endings at all. They have not alternative endings, they have different kinds of fail states or consolation endings and a true ending. Hah. Some games even spell out how the ending is called, like the good ending, the bad ending, the true ending and so on. Or they call what happened to side characters a "different" ending. Nah. That is not a different ending, that is details of the ending. It would be elegant to import from the previous game, for continuation. But the actual ending would be, the hero defeated the villain, did he not? How would you multiply that? The hero did not win? That is usually called game over and people load a save game and try again.