This popup was recently introduced in PR-2174.
I don't know exactly why, but voyager prompting me that I'm about to lose my progress was sort of strange to me in the context of scrolling on lemmy.
I understand why someone wants such a feature, but IMO this should be turned off by default and available as an option.
Just check the box, move on.
We asked for it to be on by default and have a "don't ask me again" checkbox. That's what we got.