A common question to this platform so you can have a search on answers already given, but in summary:
Yes the Contractor shows effects of non-implemented compensation events - how can they not? If the PM has instructed them to do something that is a change to the Works Information and requested a quote under 61.1, they are proceeding with those works. These may already be affecting the planned works, yet will be several weeks before the quote is agreed and hence implemented. If a Contractor has been instructed not to work in an area for the next two weeks which is a CE - they have to show that. The key here is that they should only affect planned Completion, not Completion Date. If the effect is to delay planned Completion by three weeks, planned Completion moves three weeks beyond the Completion Date. When the quote is agreed, it includes the assessment of time. If the PM agrees three weeks then Completion Date can now move and catch up with planned. If the assessment is only two weeks, then planned Completion will be one week beyond the Completion Date and Contractor liable for Delay Damages if they can not recover the time (or they go adjudication to claim the extra week if they believe they are correct). This is why we have the separation of the two milestones. Planned Completion reflects REALITY, whilst Completion Date indicates LIABILITY.
Early Warnings are a bit different. The Contract used to say you show the effects of notified early warning matters on the programme, but this was taken out in 2006 as Contractors were showing potential effects of uncertain events on the programme. Therefore these should not be shown/driving the programme, but for the reasons above non-implemented compensation events absolutely should absolutely be shown (but only initially effect planned Completion).
n.b. to not show instructed works that is agreed is a CE but not yet implemented would be a reason to reject the programme under clause 31.3 as it would be unrealistic!