diff --git a/readthedocs/api/v2/utils.py b/readthedocs/api/v2/utils.py
index 011a10cd057..1155c385fb1 100644
--- a/readthedocs/api/v2/utils.py
+++ b/readthedocs/api/v2/utils.py
@@ -28,6 +28,7 @@ def sync_versions_to_db(project, versions, type):
 
     - check if user has a ``stable`` / ``latest`` version and disable ours
     - update old versions with newer configs (identifier, type, machine)
+    - take into account ``VersionOverride`` for versions modified by the user
     - create new versions that do not exist on DB (in bulk)
     - it does not delete versions
 
@@ -77,17 +78,20 @@ def sync_versions_to_db(project, versions, type):
                 # Version is correct
                 continue
 
-            # Update slug with new identifier
-            Version.objects.filter(
+            # Update slug with new identifier if it differs
+            v = Version.objects.filter(
                 project=project,
                 verbose_name=version_name,
                 # Always filter by type, a tag and a branch
                 # can share the same verbose_name.
                 type=type,
-            ).update(
-                identifier=version_id,
-                machine=False,
-            )
+            ).first()
+
+            # Update the version with VCS data only if the version is not
+            # overridden by the user
+            if v and not v.active or (not v.override or not v.override.user_identifier):
+                v.machine = False
+                v.identifier = version_id
 
             log.info(
                 "Re-syncing versions: version updated.",
diff --git a/readthedocs/builds/forms.py b/readthedocs/builds/forms.py
index b5d3084f764..bc67cde05f5 100644
--- a/readthedocs/builds/forms.py
+++ b/readthedocs/builds/forms.py
@@ -21,6 +21,7 @@
     RegexAutomationRule,
     Version,
     VersionAutomationRule,
+    VersionOverride,
 )
 
 
@@ -30,6 +31,8 @@ class Meta:
         states_fields = ["active", "hidden"]
         privacy_fields = ["privacy_level"]
         fields = (
+            "slug",
+            "identifier",
             *states_fields,
             *privacy_fields,
         )
@@ -89,6 +92,15 @@ def _is_default_version(self):
         return project.default_version == self.instance.slug
 
     def save(self, commit=True):
+        # Recover the original data from DB to save it as backup
+        version = Version.objects.get(pk=self.instance.pk)
+        override, _ = VersionOverride.objects.get_or_create(version=version)
+        override.user_slug = self.instance.slug
+        override.user_identifier = self.instance.identifier
+        override.original_slug = version.slug
+        override.original_identifier = version.identifier
+        override.save()
+
         obj = super().save(commit=commit)
         obj.post_save(was_active=self._was_active)
         return obj
diff --git a/readthedocs/builds/migrations/0060_change_slug_identifier.py b/readthedocs/builds/migrations/0060_change_slug_identifier.py
new file mode 100644
index 00000000000..eb7e8722b8c
--- /dev/null
+++ b/readthedocs/builds/migrations/0060_change_slug_identifier.py
@@ -0,0 +1,34 @@
+# Generated by Django 4.2.16 on 2024-12-02 15:05
+
+from django.db import migrations, models
+import django.db.models.deletion
+import django_extensions.db.fields
+from django_safemigrate import Safe
+
+
+class Migration(migrations.Migration):
+    safe = Safe.before_deploy
+
+    dependencies = [
+        ('builds', '0059_add_version_date_index'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='VersionOverride',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', django_extensions.db.fields.CreationDateTimeField(auto_now_add=True, verbose_name='created')),
+                ('modified', django_extensions.db.fields.ModificationDateTimeField(auto_now=True, verbose_name='modified')),
+                ('original_slug', models.CharField(blank=True, max_length=255, null=True)),
+                ('user_slug', models.CharField(blank=True, max_length=255, null=True)),
+                ('original_identifier', models.CharField(blank=True, max_length=255, null=True)),
+                ('user_identifier', models.CharField(blank=True, max_length=255, null=True)),
+                ('version', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, related_name='override', to='builds.version')),
+            ],
+            options={
+                'get_latest_by': 'modified',
+                'abstract': False,
+            },
+        ),
+    ]
diff --git a/readthedocs/builds/models.py b/readthedocs/builds/models.py
index ffc34333781..e7ba8cf04b6 100644
--- a/readthedocs/builds/models.py
+++ b/readthedocs/builds/models.py
@@ -86,6 +86,45 @@
 log = structlog.get_logger(__name__)
 
 
+class VersionOverride(TimeStampedModel):
+    """
+    User-modified ``Version`` of a ``Project``.
+
+    We use this model to store all the fields the user has override from the
+    original ``Version`` and also to keep those original values.
+
+    This model allows us to perform a re-sync of VCS versions.
+    """
+
+    version = models.OneToOneField(
+        "Version",
+        related_name="override",
+        on_delete=models.CASCADE,
+    )
+    # TODO: add validations to `_slug` fields. We can't use `VersionSlugField`
+    # because it requires the `populate_from` field that we don't need here.
+    original_slug = models.CharField(
+        max_length=255,
+        null=True,
+        blank=True,
+    )
+    user_slug = models.CharField(
+        max_length=255,
+        null=True,
+        blank=True,
+    )
+    original_identifier = models.CharField(
+        max_length=255,
+        null=True,
+        blank=True,
+    )
+    user_identifier = models.CharField(
+        max_length=255,
+        null=True,
+        blank=True,
+    )
+
+
 class Version(TimeStampedModel):
 
     """Version of a ``Project``."""