diff --git a/core/src/main/java/org/apache/iceberg/MetadataUpdate.java b/core/src/main/java/org/apache/iceberg/MetadataUpdate.java
index ba038c196e43..65282302b5f9 100644
--- a/core/src/main/java/org/apache/iceberg/MetadataUpdate.java
+++ b/core/src/main/java/org/apache/iceberg/MetadataUpdate.java
@@ -338,7 +338,11 @@ public String name() {
 
     @Override
     public void applyTo(TableMetadata.Builder metadataBuilder) {
-      metadataBuilder.removeRef(refName);
+      if (refName.equals(SnapshotRef.MAIN_BRANCH)) {
+        metadataBuilder.resetMainBranch();
+      } else {
+        metadataBuilder.removeRef(refName);
+      }
     }
   }
 
diff --git a/core/src/main/java/org/apache/iceberg/TableMetadata.java b/core/src/main/java/org/apache/iceberg/TableMetadata.java
index 9f6ffbcc8714..77bbfaff64e0 100644
--- a/core/src/main/java/org/apache/iceberg/TableMetadata.java
+++ b/core/src/main/java/org/apache/iceberg/TableMetadata.java
@@ -1297,7 +1297,7 @@ public Builder removeRef(String name) {
       return this;
     }
 
-    private Builder resetMainBranch() {
+    protected Builder resetMainBranch() {
       this.currentSnapshotId = -1;
       SnapshotRef ref = refs.remove(SnapshotRef.MAIN_BRANCH);
       if (ref != null) {