To understand clause 61.3, you need to read and understand clause 61.1. This sets out the compensation events that the you as project manager are required to notify. You should know about all of them because they have arisen as a result of your (or the supervisor’s) actions. Therefore, the time bar will not apply to those compensation events. After all, why should the contractor suffer because you have not done what clause 61.1 says you should have done?
Clause 61.3 allows the contractor to notify any compensation event it wishes to, including a compensation event which you should have notified but failed to. However, the time bar for that notification only applies to compensation events which you were not required to notify.
If you look at pages 73 and 74 of the ECC Guidance Notes (2013 edition), it gives guidance – by reference to the subclasses numbers of clause 60.1 – as to which categories of compensation events you should notify, and which therefore the time bar does not apply to, and which categories of compensation events the time bar does apply to.
The moral of all of this is that you should do what the contract requires in respect of notifying compensation events that have arisen from your actions. If you do not do so, then the contractor can come back much later and notify them.