Personally, I have gone through so many productivity note-taking apps that mine are now plain-texts[1] with a tool that can read them. Of course, the texts are spiced with a tad of Markdown for readability and for the tools to make it easier on the eye. Right now, I'm with Obsidian.[2] However, I can move to any tool that does not chew up my content but just does its thang on top of it.
I also use iA Writer[3] a lot when picking out just a single file to focus on.