I fixed this in my own toplevel by adding an #init.  Here's the code:

(* To init the toplevel env *)
let _ = Hashtbl.add directive_table "init" (Directive_none
                                              (fun () -> Env.reset_cache ();
                                                toplevel_env := Compile.initial_env()))

Just add that somewhere in toplevel/topdirs.ml and #init;; will clear out the environment.  It turns out the Env module's hash cache of the .cmi CRCs is what was preventing a reload of my file.  Not sure if that's a bug or not.

Chris

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