I don’t know how to change settings across folders. If I manually implement pagination, any increase or decrease in manuscript length will mean I have to repaginate each folder / chapter. Any help would be much appreciated.
The Master Document Feature is designed to provide this type of function. There is some information to be found with help. Chapter 13 of the LibreOffice Writer Guide is called working with Master Documents and I find the chapter and the whole manual very useful. I personally prefer the printed paper version you can order from Lulu.com. See https://wiki.documentfoundation.org/Documentation/Publications for more information.