FIDIC: Which are the mechanisms in the Silver Book to revoke a previously instructed Variation?

The case is more elaborate but I’ll shorten it as much; Under the provisions of our Contract, SC 7.8 [Royalties], the Contractor has to pay the royalties for the materials outside the Site needed to complete the Works. Despite that, and without the Employer’s Representative presence/assignment then (early stage of the Project), a Variation was instructed for payment of the incurred Cost for royalties.
Considering the above: Which are the mechanisms in the Silver Book to revoke a previously instructed Variation, if any?

That depends on how the “variation” came about. If it was as between the Employer and Contractor direct then the contract will not have a mechanism for the reversal of that agreement. The parties would have to reach a separate agreement and of course why would the contractor do that.

Generally once a variation is instructed it cannot be “revoked”. What you can do is reverse it with a subsequent variation but that reversing variation must be priced. Here that price is likely to be the royalty value so it would achieve little .