Solved. This was expected, it's by design. See below.
Found the https://lingva.adminforge.de in my Vanadium's bookmarks. After removing the pop-up confirmation didn't reoccur. Thanks for the hint, @Dumdum.
Looks like Vanadium uses an extra confirmation step for important (bookmarked) sites before deleting the temporary data from them. I haven't noticed this before, maybe because I don't use bookmarks in Vanadium.