[EDIT: updated to apply to undirected graphs]
Lemma 1. The general problem (with $r$ given as input) is solvable in polynomial time.
Proof. 1. Fix a problem instance $(G=(V, E), s, t)$.
For brevity, define an $r$-cut to be any edge subset $C\subseteq E$
such that every $s$-$t$ path contains at least $r$ edges in $C$.
The goal is to find a minimum-size $r$-cut. (Note that we use $E$ for the given edge set, and $C$ for the solution, whereas the post uses $E$ for the solution.)
- Consider the following linear-program (LP) relaxation of the problem:
$$\begin{aligned}
\textsf{minimize } &\textstyle ~\sum_{e\in E} \ell_e~ \textsf{ s.t.}\\
\pi_s &{} = 0 \\
\pi_t &{} \ge r \\
|\pi_w - \pi_u| & {} \le \ell_e \le 1 && (e=\{u,w\} \in E)
\end{aligned}
$$
Note that the LP is indeed a relaxation of the original problem.
Indeed, each solution $C$ to the given instance
corresponds to the integer-valued LP solution $(\ell, \pi)$ of cost $|C|$
obtained by setting $\ell_e = 1$ for $e\in C$, and setting
each $\pi_v$ to the distance from $s$ to $v$ in the graph
where each edge $e$ is assigned length $\ell_e$.
Conversely, given any integer-valued feasible LP solution $(\ell, \pi)$,
taking $C=\{e \in E : \ell_e = 1\}$ gives a solution $C$
to the given instance, of size $|C|=\sum_{e\in E} \ell_e$.
Now, using any polynomial-time LP algorithm,
compute a min-cost (possibly fractional) solution $(\ell, \pi)$
to the LP.
Since the LP is a relaxation of the original problem,
the cost $\sum_{e\in E} \ell_e$ of $(\ell, \pi)$ is a lower bound
on the minimum size of any $r$-cut.
Compute a random integer LP solution $(\ell', \pi')$ and corresponding $r$-cut $C$ from $(\ell, \pi)$
using the following randomized-rounding scheme:
- choose $\lambda \in [0, 1)$ uniformly at random
- let $\pi'_v = \lfloor \pi_v + \lambda \rfloor$ for each vertex $v\in V$
- let $\ell'_e = |\pi'_w - \pi'_u|$ for each edge $e=\{u,w\}\in E$
- let $C=\{e\in E: \ell'_e = 1\}$ be the $r$-cut corresponding to $(\ell', \pi')$
First observe that $(\ell', \pi')$ is feasible.
In particular, for any edge $\{u, w\}\in E$, we have
$$\ell'_e = |\pi'_w - \pi'_u| =
|\lfloor \pi_w + \lambda \rfloor -
\lfloor \pi_u + \lambda \rfloor| \le 1$$
because $|(\pi_w + \lambda) - (\pi_u + \lambda)| \le \ell_e \le 1$.
Next we bound the expected size of $C$.
Consider any edge $e=\{u,w\}\in E$.
We will show $\Pr[e\in C] \le \ell_e$.
Note $|\pi_w - \pi_u| \le \ell_e \le 1$, so
$$\Pr[e\in C]
= \Pr_\lambda[|\lfloor \pi_w + \lambda \rfloor
- \lfloor \pi_u + \lambda \rfloor| = 1]
= |\pi_w - \pi_u| \le \ell_e.
$$
(The second equality above follows by calculation.)
So $\Pr[e\in C] \le \ell_e$ for all $e\in E$.
Now, using also linearity of expectation, we have
$E[|C|] = \sum_{e\in E} \Pr[e\in C] \le \sum_{e\in E} \ell_e$.
That is, the expected size of the $r$-cut $C$ is at most
the cost of $(\ell, \pi)$. Since the latter cost is at most
OPT (the minimum size of any $r$-cut), it follows that
the expected size of $C$ is at most OPT. $~~~~\Box$
BTW, since $|C|$ can't be less than OPT in any outcome,
it follows that $C$ must be optimal, for any choice of
$\lambda\in [0, 1)$. Essentially, every optimal solution
to the LP is a convex combination of optimal integer solutions.