There is at least a randomized $O(n^4)$ time algorithm. To make sure the specified arc $uv$ is part of the cycle cover, contract the arc into one vertex $w$ retaining $u$'s ingoing arcs and $v$'s outgoing arcs.
Take the adjacency matrix $A$ of the resulting graph, replace each arc (i.e. $1$) with a random number, introduce an indeterminate $r$ and compute $p(r)=\operatorname{det}(J*r+A)$, where $J$ is the identity matrix except for the element corresponding to the vertex $w$, where it is zero. The smallest exponent $e$ such that the monomial $r^e$ has a non-zero coefficient in $p(r)$ is "proof" of the fact that there is an induced subgraph on $n-e$ vertices that has a cycle cover containing your arc. Conversely, if there are cycle covers on $n-e$ vertices, the coefficient of $r^e$ is most probably not zero.
Look at Edmonds matrix, and note that perfect matchings in balanced bipartite graphs is in one-to-one correspondence with cycle covers in digraphs. See also Schwartz-Zippel to see how to bound the probability of failures.