If the EIR is accepted by the European Parliament
It is the Regulation as a whole that is subject to scrutiny by the European Parliament and the Council. They cannot reject the EIR and keep the rest of the Regulation. They can only vote to oppose the adoption of the Regulation in it entirety on certain legal and procedural grounds. If that happens the CBM IR, Article 4(8) and the extension of the derogation for third country licence holders would also be lost. Given that there does not appear to be anyone lobbying against the Regulation it is hard to imagine that it will be rejected.
So far as I am aware, EP scrutiny has lead to only one motion to oppose the adoption of a Commission Regulation giving effect to EASA implementing rules. That was on flight time limitations. The motion was defeated in the vote.