I don't know whether this is specifically a Prelude issue, but: in Emacs 27.x, the keys shift-{up,down,left,right} in org-mode are mapped to org-shift{up,down,left,right}. In 28.1 the same keys are bound globally to windmove-{up,down,left,right} and take precedence.

I like having windmove-* available so have temporarily bound the org-mode shift-* functions to alt-{up,down,left,right} instead. Am happy to put in a pull request if there's a consensus about what bindings are most acceptable.