If a member state fails to block a proposal, all that simply means is that the qualified majority[1] of representatives of other member states believes the legislation to be so important that the union would not work without it. Dissenting member states can seek to reverse or temper the legislation later, or simply leave the union - see Brexit. No sovereignty is violated at any point.
[1]: https://en.wikipedia.org/wiki/Voting_in_the_Council_of_the_E...