In preferences > Folder Tree > Pins, it says that "Pinned branches are permanently expanded". but if I close and re-open Opus, the branches are no longer expanded.
Expanded folders can be saved to layouts if the options under Preferences / Folder Tree / Expand/Collapse / Remember expanded root items in layouts are turned on.
The pin state is saved per layout (or when you explicitly save the tree's current state as a preset for the tree itself).
This lets you pin different folders in different windows. But may also mean you have to save the change if you're using layouts, or have turned off auto-saving of the Default Lister.
Where it says "permanently expanded", it means the branches will stay expanded forever (or until unpinned) and cannot be collapsed within that window.