Wow, I am shocked at how easy that was. Patch mu to not update dups

common/mu.patch

@@ -0,0 +1,15 @@
+diff --git a/lib/mu-store.cc b/lib/mu-store.cc
+index c67b551c..59eb183c 100644
+--- a/lib/mu-store.cc
++++ b/lib/mu-store.cc
+@@ -582,7 +582,7 @@ Store::move_message(Store::Id id,
+ 		const auto dup_flags{filter_dup_flags(dup_msg->flags(), *new_flags)};
+ 		/* use the updated new_flags and MoveOptions without DupFlags (so we don't
+ 		 * recurse) */
+-		opts = opts & ~MoveOptions::DupFlags;
++		opts = opts & ~MoveOptions::DupFlags & ~MoveOptions::ChangeName;
+ 		if (auto dup_res = priv_->move_message_unlocked(
+ 			    std::move(*dup_msg), Nothing, dup_flags, opts); !dup_res)
+ 			mu_warning("failed to move dup: {}", dup_res.error().what());
+--
+2.51.2

common/overlays.nix

@@ -19,7 +19,13 @@ inputs: system:
       ((prev.emacsPackagesFor final.emacs-unstable)
         .emacsWithPackages (epkgs: with epkgs; [
           treesit-grammars.with-all-grammars
-          mu4e
+          (mu4e.override (prev: {
+            mu = prev.mu.overrideAttrs (old: {
+              patches = (old.patches or []) ++ [
+                ./mu.patch
+              ];
+            });
+          }))
         ]));
   })