diff --git a/homeassistant/config_entries.py b/homeassistant/config_entries.py
index 25608568202..2781dea529e 100644
--- a/homeassistant/config_entries.py
+++ b/homeassistant/config_entries.py
@@ -2147,7 +2147,12 @@ class ConfigEntries:
         if unique_id is not UNDEFINED and entry.unique_id != unique_id:
             # Deprecated in 2024.11, should fail in 2025.11
             if (
-                unique_id is not None
+                # flipr creates duplicates during migration, and asks users to
+                # remove the duplicate. We don't need warn about it here too.
+                # We should remove the special case for "flipr" in HA Core 2025.4,
+                # when the flipr migration period ends
+                entry.domain != "flipr"
+                and unique_id is not None
                 and self.async_entry_for_domain_unique_id(entry.domain, unique_id)
                 is not None
             ):
@@ -2425,6 +2430,12 @@ class ConfigEntries:
             issues.add(issue.issue_id)
 
         for domain, unique_ids in self._entries._domain_unique_id_index.items():  # noqa: SLF001
+            # flipr creates duplicates during migration, and asks users to
+            # remove the duplicate. We don't need warn about it here too.
+            # We should remove the special case for "flipr" in HA Core 2025.4,
+            # when the flipr migration period ends
+            if domain == "flipr":
+                continue
             for unique_id, entries in unique_ids.items():
                 # We might mutate the list of entries, so we need a copy to not mess up
                 # the index
diff --git a/tests/test_config_entries.py b/tests/test_config_entries.py
index e3594269b58..d530628d27c 100644
--- a/tests/test_config_entries.py
+++ b/tests/test_config_entries.py
@@ -7118,6 +7118,41 @@ async def test_async_update_entry_unique_id_collision(
     assert issue_registry.async_get_issue(HOMEASSISTANT_DOMAIN, issue_id)
 
 
+@pytest.mark.parametrize("domain", ["flipr"])
+async def test_async_update_entry_unique_id_collision_allowed_domain(
+    hass: HomeAssistant,
+    manager: config_entries.ConfigEntries,
+    caplog: pytest.LogCaptureFixture,
+    issue_registry: ir.IssueRegistry,
+    domain: str,
+) -> None:
+    """Test we warn when async_update_entry creates a unique_id collision.
+
+    This tests we don't warn and don't create issues for domains which have
+    their own migration path.
+    """
+    assert len(issue_registry.issues) == 0
+
+    entry1 = MockConfigEntry(domain=domain, unique_id=None)
+    entry2 = MockConfigEntry(domain=domain, unique_id="not none")
+    entry3 = MockConfigEntry(domain=domain, unique_id="very unique")
+    entry4 = MockConfigEntry(domain=domain, unique_id="also very unique")
+    entry1.add_to_manager(manager)
+    entry2.add_to_manager(manager)
+    entry3.add_to_manager(manager)
+    entry4.add_to_manager(manager)
+
+    manager.async_update_entry(entry2, unique_id=None)
+    assert len(issue_registry.issues) == 0
+    assert len(caplog.record_tuples) == 0
+
+    manager.async_update_entry(entry4, unique_id="very unique")
+    assert len(issue_registry.issues) == 0
+    assert len(caplog.record_tuples) == 0
+
+    assert ("already in use") not in caplog.text
+
+
 async def test_unique_id_collision_issues(
     hass: HomeAssistant,
     manager: config_entries.ConfigEntries,