This question seems to relate more to the Specification for Highways Works than it does to the NEC3. However, as a SHW user, and while it is difficult to comment fully without seeing your Works Information, I would answer as follows;
The Client appears to have attempted to compile Appendix 0/3 by marking those Appendices that they have not used as "Not Used". This is a generally accepted method of completing Appendix 0/3 although the notes regarding the Compiler adding "Not Used" were removed in 2014.
Where a particular Specification "Series" is not required in the Works the Appendices would have been marked as "Not Used" to confirm their status and clarify that they are not missing or included in another document. If a Vehicle Restraint System renewal scheme does not involve, say, new bridge bearings, Appendix 22/1 would be marked "Not Used," refer to Clause 10 of the Standard Preamble
Appendix 0/1 is used to add entirely new Contract specific clauses, revise existing SHW clauses or cancel a clause where it conflicts with something the Client has added elsewhere. Clauses which are not used, say bridge bearings in my example, would not be marked as cancelled in Appendix 0/1 but you would ignore them given that there are no bearings to install, refer to Clause 9 of the Standard Preamble.
Of course, should the Client amend the Works Information at any time then it would become a positive or negative Compensation Event under 60.1(1).