In October 2017 the NEC issued guidance around what they meant with their amended NEC4 clause 63.5, and then finally in 2019 version of NEC4 they have amended the wording of the contract clause 63.5 to make it very clear how it is assessed. It states now:
The assessment takes into account:
- any delay caused by the compensation event already in the Accepted Programme, and
- events which have happened between the date of the Accepted Programme and the dividing date
Point 1 would therefore cover your issue, where if the last accepted programme showed a two week delay, you can still retrospectively demonstrate that the two weeks was due to a CE that has only just been (say) notified.