The closest guidance I could find is related to cleaning out meetinghouse resource centers. See
Resource Centers – click where it says "Procedures for Adding and Discarding Materials." Some of the FAQs are also relevant.
Basically, unneeded, unnapproved, and/or unused items should be discarded. They can be given to other meetinghouses, offered to members, donated to Deseret Industries or another thrift store (though they likely won't take a whole box), thrown away, or recycled.
I don't see anything about what to do with manuals in the clerk's office or bishop's office – but that's an easy fix: Put them in the resource center, then the resource center guidelines will apply.
