If an ambiguity or inconsistency on Works Information (NEC ECC Option E) is raised by the Contractor under Clause 17.1, and the Project Manager gives instruction resolving the ambiguity under Clause 17.1, although the instruction adds further information which effectively amends/adds to the Works Info, does the Project Manager also need to instruct this additional information under Clause 14.3?
The answer is yes as, from what you have said, there has been a change to the Works Information. This could also be a compensation event under clause 60.1 (1) which the PM should also notify, unless one of the corresponding bullet points applies.
Further to my answer, the PM does not instruct a change specifically referring to clause 14.3, as what this clause does is give the PM authority to instruct such a change to the Works Information. For clarity, however, the PM would be well advised to state whether the instruction is a change to the WI and further notify a compensation event, where appropriate. This would then resolve any misunderstanding, which has clearly occurred in your situation.