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This is a known issue with SimpylFold (https://github.com/tmhedberg/SimpylFold/issues/116) I still use it because I think it gives the best folding, but I also have a snippet in ~/.vim/after/ftplugin/python.vim which recalculates folds when saving the document, making this bug less annoying
I use a custom foldexpr. I've been using it for many years, and polished it to do the right thing on all the codebases I've used it on.
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