Yes that should be doable, at least in the case where the (fold), (end) pair is used, once we capture that case in the grammar. The reason it works with environments is because I can set the input to the current scope, so provided each entire section gets its own scope, it should be doable. Similarly, the Change Environment command could be made to work for sections as well, allowing you to quickly change a section to, say, a subsection, with automatic renaming of the label prefix as well as the % section (end) part.

I would also suggest that you make the fold marks specific to that part, i. e. (end section) or something like that.

Not only does it make the code more readable, but I suppose it's also easier to filter and look for the right (end) …

Max