diff --git a/src/main/scala/firrtl/transforms/MustDedup.scala b/src/main/scala/firrtl/transforms/MustDedup.scala
index 3e7629cda7..cce6764325 100644
--- a/src/main/scala/firrtl/transforms/MustDedup.scala
+++ b/src/main/scala/firrtl/transforms/MustDedup.scala
@@ -14,18 +14,21 @@ import firrtl.graph.DiGraph
 import java.io.{File, FileWriter}
 
 /** Marks modules as "must deduplicate" */
-case class MustDeduplicateAnnotation(modules: Seq[IsModule]) extends MultiTargetAnnotation {
-  def targets: Seq[Seq[IsModule]] = modules.map(Seq(_))
-
-  def duplicate(n: Seq[Seq[Target]]): MustDeduplicateAnnotation = {
-    val newModules = n.map {
-      case Seq(mod: IsModule) => mod
-      case _ =>
-        val msg = "Something went wrong! This anno should only rename to single IsModules! " +
-          s"Got: $modules -> $n"
-        throw new Exception(msg)
+case class MustDeduplicateAnnotation(modules: Seq[IsModule]) extends Annotation {
+
+  def update(renames: RenameMap): Seq[MustDeduplicateAnnotation] = {
+    val newModules: Seq[IsModule] = modules.flatMap { m =>
+      renames.get(m) match {
+        case None => Seq(m)
+        case Some(Seq()) => Seq()
+        case Some(Seq(one: IsModule)) => Seq(one)
+        case Some(many) =>
+          val msg = "Something went wrong! This anno's targets should only rename to IsModules! " +
+            s"Got: ${m.serialize} -> ${many.map(_.serialize).mkString(", ")}"
+          throw new Exception(msg)
+      }
     }
-    MustDeduplicateAnnotation(newModules)
+    if (newModules.isEmpty) Seq() else Seq(this.copy(newModules))
   }
 }
 
diff --git a/src/test/scala/firrtlTests/transforms/MustDedupSpec.scala b/src/test/scala/firrtlTests/transforms/MustDedupSpec.scala
index 2f633e0e52..5d25321eb7 100644
--- a/src/test/scala/firrtlTests/transforms/MustDedupSpec.scala
+++ b/src/test/scala/firrtlTests/transforms/MustDedupSpec.scala
@@ -264,4 +264,38 @@ class MustDedupSpec extends AnyFeatureSpec with FirrtlMatchers with GivenWhenThe
       (new firrtl.stage.FirrtlPhase).transform(annos)
     }
   }
+
+  Feature("When you have unused modules that should dedup, and they do") {
+    val text = """
+                 |circuit A :
+                 |  module B :
+                 |    output io : { flip in : UInt<8>, out : UInt<8> }
+                 |    io.out <= io.in
+                 |  module B_1 :
+                 |    output io : { flip in : UInt<8>, out : UInt<8> }
+                 |    io.out <= io.in
+                 |  module A :
+                 |    output io : { flip in : UInt<8>, out : UInt<8> }
+                 |    inst b of B
+                 |    inst b_1 of B_1
+                 |    b.io.in <= io.in
+                 |    b_1.io.in <= io.in
+                 |    io.out <= and(io.in, UInt(123))
+    """.stripMargin
+    val top = CircuitTarget("A")
+    val bdedup = MustDeduplicateAnnotation(Seq(top.module("B"), top.module("B_1")))
+
+    Scenario("MustDeduplicateAnnotation should be deleted gracefully") {
+      val testDir = createTestDirectory("must_dedup")
+      val annos = Seq(
+        TargetDirAnnotation(testDir.toString),
+        FirrtlSourceAnnotation(text),
+        RunFirrtlTransformAnnotation(new MustDeduplicateTransform),
+        bdedup
+      )
+
+      val resAnnos = (new firrtl.stage.FirrtlPhase).transform(annos)
+      resAnnos.collectFirst { case a: MustDeduplicateTransform => a } should be(None)
+    }
+  }
 }