Under the 'Tree and List' settings, I unchecked 'Show Links folder', 'Show Document folder' and 'Show OneDrive folder'.
But when visiting those folders (for example via 'This PC > Links' or 'Links > Documents', they are automatically added back into the tree (while still unchecked in the 'Configuration'). They then need to be manually hidden from the tree again.
Unchecked/hidden folders reappearing in tree
Re: Unchecked/hidden folders reappearing in tree
It sounds like you are in MiniTree mode, to which those settings don't apply.