Let's suppose that we have two orthonormal basis, $V=\{|v_i\rangle \}$, $i=1,...n$ (ket notation) and $U=\{|u_j\rangle\}$, $j=1,..,m$, with $m<n$ (i.e. $\dim U< \dim V$), where $|u_j\rangle=\sum_{i=1}^{n}c_i^j |v_i\rangle$. Given that $[A]_V$ is the matrix representation of some transformation $A$ in the basis $V$, under which conditions $[A]_U$ is the matrix representation of the same transformation $A$ in the basis $U$?
$$[A]_{U}=\left[ \begin{array}{c} \langle u_1| \\ \vdots\\ \langle u_m| \end{array} \right] [A]_{V}\left[ \begin{array}{c} |u_1\rangle & \cdots & |u_m\rangle| \end{array} \right]$$
A linear transformation $A$ acts on a vector space $X$. If the $X$ is finite dimensional, then every basis of $X$ has the same number of vectors (which is equal to $\dim X$). Hence, your question doesn't make sense from the start: you cannot have two (orthonormal) bases of $X$ with different numbers of basis vectors.