This is effectively a 'loss and expense' type claim, which under other forms of contract would be dealt with separately from the variation entitlement, although under NEC is required to be included within a CE quotation.
It seems that what you have identified is the consequential effect of previous compensation events on the contracted scope of works, whereby the rates in the BoQ no longer represent what is actually occurring on Site.
What usually occurs is that the cumulative effect of CE's means that you now require additional resources, either People or Equipment, to manage the works, although this in itself is not a CE. It is often caused by the disrupting influence of previous CEs although is difficult to conclusively prove as there will usually be other such events which are a (Sub) contractor's risk, such as (non CE) weather, Equipment breakdowns or availability etc.
An analysis of the programme for each CE is essential to assess the possible impact of each event and to make an appropriate allowance, even if included as a risk allowance for disruption. This will almost certainly not be accepted by the PM / Contractor as it is not an 'obvious' effect, even though disruption is a very real issue (see the Society of Construction Law's Delay and Disruption Protocol for details).
Assessing the value of disruption is difficult after the event so even more so beforehand, although does fit better with the requirements of a CE quotation as it complies with the 'significant chance of occurring' and are 'not compensation event' tests. This creates a further problem with how you price such risks as a quotation is required to be priced on the basis of Defined Cost, so an arbitrary percentage addition almost certainly wouldn't comply with this requirement, unless agreed.
Each time you are pricing a CE you are assessing the combined disrupting affect of every CE and apportioning an amount within the quotation. Not an easy principle to 'prove' although it is based on the 'balance of probabilities' so a programme assessment should be a good starting point and highlights the importance of managing the programme under an NEC contract.
If you can agree, an instruction to change the Works Information (as suggested by Jon Broome) to add additional resources (People or Equipment) would be a simple way to deal with this matter.