Can I lose a variation claim by notifying it late?

Yes, where the contract makes giving notice in time a condition of being paid at all, and NEC contracts are built that way on purpose. A notice here is simply a formal written warning, given within a set period, that an event has happened or a claim is coming. The key thing to look for is condition precedent wording, contract language saying that giving the notice in time is a precondition of the entitlement itself. Where a contract is drafted that way, a claim notified late can fail on timing alone, however strong it would have been on the facts, which reflects the parties' agreement to deal with problems while they are fresh. Where the wording is softer and notice is not made a strict precondition, being late does not automatically destroy the claim, but it still costs you: it goes to how believable the claim is, and the further it sits from the event, the thinner your records and the easier it is for the other side to deny it. Because you often cannot tell at a glance which kind of clause you are under, notify first, in the form and to the recipient the contract requires, and perfect the detail afterwards, so a timing point can never be used to defeat you.

Say a steelwork contractor is held up for three weeks when the employer fails to give access to the site as promised. The contractor knows it has a good claim for the delay and the extra cost, but is busy, so it decides to gather every timesheet and cost sheet into a polished submission before saying anything. By the time that bundle lands, ten weeks have passed. Buried in the contract is a clause saying the contractor must notify any such claim within, say, four weeks of the event or lose the right to it, which is condition precedent wording. Because the notice came late, the employer rejects the whole claim on timing, and the strength of the underlying facts never gets tested. Had the contractor sent a short holding notice in the first days, flagging that the access failure had caused delay from the Monday with full particulars to follow, the deadline would have been met and the detailed submission could have followed at leisure. Notify first and perfect the paperwork second.