This will certainly work fine in finite type. Folding $Q$ to $Q'$ corresponds to an inclusion of $W'$ into $W$, where the reflections of $W'$ are mapped to products of commuting reflections in $W$. $c'$-sortable elements of $W'$ give you a sublattice of the $c$-sortable elements of $W$. Thus, if you take a maximal green sequence for $W'$, you get an increasing sequence of $c$-sortable elements in $W$. You can then refine this to a maximal green sequence in $W$. You can typically refine it in more than one way, of course.
(Edited to add:) Conversely, suppose we start with a maximal green sequence for $W$. There is a lattice quotient of the $c$-Cambrian lattice which sends each $c$-sortable to the maximum $c'$-sortable in the image of $W'$ below it. Since this is a lattice quotient, general results of Reading imply that it corresponds to a coarsening of the $c$-Cambrian fan for $W$, which is isomorphic to the $c'$-Cambrian fan. The maximal green sequence for $W$ can be thought of as a positively oriented path through the $c$-Cambrian fan. It induces a positively oriented path through the coarsened fan, which is a maximal green sequence for $W'$.
This gives us a way to fold any maximal green sequence for $W$ to obtain a maximal green sequence for $W'$.