1) Let us for simplicity put various constants to one: Speed of light $c=1$; Planck constant $\hbar=1$; Mass $m=1$ of non-relativistic scalar (Bosonic) particle in $1+1$ dimensions; charge of particle $q=1$; Circumference of spatial circle $\ell=2\pi$.
2) The mechanical momentum (sometimes called the kinetic momentum)
$$\hat{v}~=~\hat{p}-A_x~=~\frac{1}{i}\partial_x-A_x~=~\frac{1}{i}D_x$$
(or equivalently, the covariant derivative) commutes with the Hamiltonian $\hat{H}=\frac{1}{2}\hat{v}^2+\Phi$ in the temporal gauge $\Phi=A^t=0$, which we will assume from now on. (Recall that $\Phi=A^t$ is the temporal component of the gauge potential.) So we can find common eigenstates. Suppressing the time dependence in what follows, we want to solve the mechanical momentum eigenvalue equation
$$\hat{v}\psi_v(x)=v \psi_v(x),$$
where the mechanical momentum eigenvalue $v\in\mathbb{R}$ is related to the energy
$E=\frac{1}{2}v^2$. The solution is $e^{ivx}$ times a Wilson line:
$$\psi_v(x)~=~ \psi_v(0)\exp\left[ivx+i\int_0^x A_x(x')dx'\right] ,\qquad v\in\mathbb{R}.$$
3) Under a local gauge transformation
$$\psi(x)\longrightarrow \tilde{\psi}(x):=e^{i\alpha(x)}\psi(x), \qquad A_x(x)\longrightarrow \tilde{A}_x(x):=A_x(x)+\partial_x\alpha(x), $$
it is well-known that the covariant derivative (or mechanical momentum) transforms covariantly,
$$D_x\psi(x)\longrightarrow e^{i\alpha(x)}D_x\psi(x), \qquad
D_x \longrightarrow \tilde{D}_x ~=~ e^{i\alpha(x)}D_x e^{-i\alpha(x)},
\qquad \hat{v}\longrightarrow e^{i\alpha(x)}\hat{v} e^{-i\alpha(x)}.$$
It is true that they are not gauge invariant. They are only gauge covariant. However, we may easily construct manifestly gauge invariant quantities, for instance, $|\psi(x)|^2$; $\psi^*(x) \hat{v}\psi(x)$. In particular, the mechanical momentum eigenvalue
$$v~=~\frac{\hat{v}\psi_v(x)}{\psi_v(x)}~=~\pm\sqrt{2E}~\in~\mathbb{R}$$
is a gauge invariant (still assuming temporal gauge $A^t=0$).
4) Finally, we assume for simplicity that $A_x(x)=A_x\in\mathbb{R}$ and $\tilde{A}_x(x)=\tilde{A}_x\in\mathbb{R}$ are independent of $x$. This corresponds to a partial gauge fixing. We still have residual gauge transformations left where $\alpha(x)$ is an affine function of $x$. The eigenfunction becomes
$$\psi_v(x)~=~ \psi_v(0)e^{i(v+A_x)x},\qquad
\tilde{\psi}_v(x)~=~ \tilde{\psi}_v(0)e^{i(v+\tilde{A}_x)x},\qquad v\in\mathbb{R}. $$
We now recall that the $x$-coordinate is periodic $x\sim x +2\pi$. The wave function should be single-valued
$$\psi_v(x+2\pi)=\psi_v(x),\qquad\tilde{\psi}_v(x+2\pi)=\tilde{\psi}_v(x),$$
so
$$v+A_x,v+\tilde{A}_x~\in~\mathbb{Z},$$
as OP observes. In other words, $A_x$ and $\tilde{A}_x$ belong to the same shifted lattice $\mathbb{Z}-v$. The residual affine function $\alpha(x)$ must have $x$-independent integer-valued derivative
$$\partial_x\alpha~=~\tilde{A}_x-A_x~=~(v+\tilde{A}_x)-(v+A_x)~\in~\mathbb{Z}.$$
5) So what have we learned?
On one hand, we may write $v\in\mathbb{Z}-A_x$, so we see that the energy $E=\frac{1}{2}v^2$ and the mechanical momentum $v$ depend on the gauge potential $A_x\in\mathbb{R}$.
On the other hand, we saw in section 3 that $E$ and $v$ are gauge invariants, i.e., they are invariant under gauge transformations (still assuming temporal gauge $A^t=0$).
The two statements (1.) and (2.) do not clash in terms of physics, only in terms of semantics. In particular, if we perform a gauge transformation on the formula $v\in\mathbb{Z}-A_x$, we cannot claim that $v$ changes since a gauge transformation changes $A_x$ by an integer. ($A_x$ itself is not necessarily an integer.)
6) Another example is the canonical momentum operator $\hat{p}=\frac{1}{i}\partial_x$.
On one hand, it is independent of the gauge potential $A_x$.
On the other hand, it is not a gauge covariant quantity, i.e., it does not transform covariantly under a gauge transformation
$$\hat{p}\longrightarrow e^{i\alpha(x)}\hat{p} e^{-i\alpha(x)}~=~\hat{p}-\partial_x\alpha(x).$$
Again, the two statements (1.) and (2.) do not clash in terms of physics, only in terms of semantics.
7) Finally, let us connect to Marek's comment. We have a Hilbert space $L^2(\mathbb{R}/\mathbb{Z})$ of wave functions on a circle $\mathbb{R}/\mathbb{Z}$, and a Heisenberg algebra $[\hat{x},\hat{v}]=i$. (More precisely, the Stone-von Neumann theorem is a statement about the corresponding Heisenberg group to avoid issues with unbounded operators.) I interpret Marek's comment as roughly saying that
$$\hat{x}=x, \qquad \hat{v}=\frac{1}{i}\partial_x-A_x,$$
yields inequivalent irreducible representations of the Heisenberg algebra labeled by a continuous label $A_x\in[0,1[$. Changing $A_x \to A_x+1$ yields an equivalent representation due to gauge symmetry.