Technician reported concerns over a procedure to dispatch an aircraft with large wing panels removed and with reference to an Engineering Authorization for a temporary speed tape repair that conflicted with the Procedures Manual.

Narrative

I am seeking clarification. On Date; Aircraft X was in ZZZ with damage to 3 inboard underwing panels. Per CDL 57-XXX the panels can be deferred as long as they are removed. Only 2 per wing. So; Engineering issued an Engineering Authorization for repair of the third panel since the CDL only states 2 can be missing. Upon flight crew walkaround; they did not like the legal CDL with the panels missing and refused to fly with the panels missing per CDL. ZZZ contacted Engineering to issue an Engineering Authorization to add speed tape to the damaged panels and reinstall the panels so the flight crew would be happy. But per Procedures Manual 24.YY.Y; it clearly states in red bold lettering; with the exception of M-procedures; Engineering cannot authorize deviation from or revisions to the MEL or CDL configuration deviation list. So; I told ZZZ we cannot use the issued Engineering Authorization for this condition because there is a legal CDL and the Procedures Manual states no deviation. We cannot sign the CDLs off in the logbook as issued [as] an Engineering Authorization. This to me; is called deviation from the CDL.The next morning on Date 1; Company Management re-writes the Procedures Manual to remove that statement and then tells ZZZ to now install the panels using the Engineering Authorization speed tape repair. My questions are when this event happened; we had the red wording in the Procedures Manual. My other question is; can [the] Company Management Team just go and change the Procedures Manual without FAA approval? I need to know this to prevent further stress; wondering if I am doing the right thing or not. I am not trying to ground any airplane; I am just trying to do things legal and in a safe manner.There were 2 underwing panels that were deferred using CDL 57-XXX and removed per the CDL instructions. The flight crew refused the aircraft that led to all this confusing. Please let Maintenance Control know the Procedures Manual edit procedures. I need to know if the FAA approves all Procedures Manual changes. Company Procedures Manual is more than just a general Procedures Manual. It's become somewhat of a repair document also.