Consider a noninteracting fermi gas of electrons. If we know the chemical potential it makes sense that the Hamiltonian is
$$\sum_{|k| > k_f} E_kc_k^{\dagger}c_k +\sum_{|k| < k_f}E_k c_kc_k^{\dagger},$$
where $E_k= |\epsilon_k - \mu|$, $\epsilon_k$ is the energy of the state with momentum $k$ and $\mu$ is the chemical potential. We're just counting holes below the fermi surface and electrons above.
This is obviously different from $\sum_k \epsilon_k c_k^{\dagger}c_k$. All we have done above is impose our knowledge of the chemical potential and use our knowledge of the corresponding ground state. We have just shifted our total energy by the energy of the state when all single-electron states below the chemical potential are filled and those above are empty. Nothing exciting going on here.
For single-particle fermions this seems like a sensible thing to do.
What I've been confused about is using this technique with interacting fermions where we don't have simple, single particle states. Consider the effective superconducting Hamiltonian,
$$H=\sum_k \epsilon_k c_k^{\dagger}c_k - \sum_k \Delta^{*} c_{-k \downarrow}c_{k \uparrow}+\Delta c_{k \uparrow}^{\dagger}c_{-k \downarrow}^{\dagger}$$
The standard technique (e.g see Annett, Superconductivity, Superfluids and Condensates and many others) is to subtract a term $\mu \hat{N} = \mu \sum_k c_k^{\dagger}c_k $, then solve for eigenstates. I don't follow the reasoning for this. My instinct would be to diagonalise before subtracting this term to get fermionic Bolgoliubov particles. Then treat these noninteracting fermionic particles as the single fermions discussed initially. I see that this doesn't lead to anything interesting around the fermi surface and as this is superconductivity, must be wrong.
I should add that I'm happy with the use of Lagrange multipliers when trying to find the ground state of a many body system with the constraint of constant particle number. Simple Lagrange multiplier knowledge can be used to show that the Lagrange multiplier used in this case is the chemical potential. But this seems (to me at least) unrelated to subtracting $\mu \hat{N}$ from a many body hamiltonian and solving for excited states.