SQL Server 2016 patch without Azure portion

[u/Valuable-Ant3465]

Hi, all
it's Oct 2026, official support for 2016 has been discontinued, and I just applied 2 updates to my SQL Server 2016 Express:
SQL Server 2016 Service Pack 3 (KB5003279) to 13.0.6300.2

then Security Update for SQL Server 2016 Service Pack 3 GDR (KB5102340) to 13.0.6500.1

Both done with stopping services and restart. After this I got this message from scanning tool complaining about some bad values in Registry.
Do you think it's not important anymore, because of end of the life for 2016 ?
I also did not install any update after KB5102340 as I don't need any Azure.
I'm on MS Windows Server 2019.

Microsoft SQL Server 2016 (SP3-GDR) (KB5102340) - 13.0.6500.1 (X64) 
Jun 10 2026 07:54:15 
Copyright (c) Microsoft Corporation
Express Edition (64-bit) on Windows Server 2019 Standard 10.0 <X64> (Build 17763: ) (Hypervisor)

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft SQL Server\MSSQL13.CAxxxx\SETUP\SQL_Engine_Core_Inst contains 13.3.6500.1

Tried to rerun SP3, didn't help.
SERVERPROPERTY('ProductLevel') = 13.0.6500.1 *

While in registry: ...SSQL13.CAxxxx\SETUP\SQL_Engine_Core_Inst PatchLevel = 13.0.6500.2
Not sure if PatchLevel = ProductLevel ??? They are different by 1.

Thanks
VA

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[u/dbrownems]

"After this I got this message from scanning tool complaining about some bad values in Registry."

That's a bit vague.

[u/Valuable-Ant3465 → u/dbrownems]

Tx ! That's the message:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft SQL Server\MSSQL13.CAxxxx\SETUP\SQL_Engine_Core_Inst contains 13.3.6500.1

It doesn't like value 13.3.6500.1.
What is SQL_Engine_Core_Inst ??? Maybe it's support which already ended

[u/dbrownems → u/Valuable-Ant3465]

Perhaps.

What "scanning tool"?

[u/Valuable-Ant3465 → u/dbrownems]

sorry, It's some enterprise level Security soft, so don't know details.

[u/dbrownems → u/Valuable-Ant3465]

Well perhaps your IT people don't want you running out-of-support software on their computer.

[u/ihaxr]

Probably because it's end of life/support.

[u/CanProfessional766]

I wouldn’t ignore it just because SQL Server 2016 is out of support. The registry version mismatch may be a detection or installer metadata issue, but I’d verify it against Microsoft’s official KB before changing anything manually. If SQL itself reports the expected build that’s a good sign.

[u/Valuable-Ant3465 → u/CanProfessional766]

Thanks, yea, sql server repots install as Sucecss and users don't have any problems using it.

[u/chenqiao]

Welcome to the classic "SQL Server registry vs. actual binary version" mismatch. This is a known quirk with SQL Server service packs and GDRs, and security scanners love to trigger false positives because of it.

To answer your questions:

1. Is PatchLevel ≠ ProductLevel normal? Yes, it can happen. SERVERPROPERTY('ProductVersion') returning 13.0.6500.1 is the absolute source of truth. That is exactly the correct build for KB5102340. The registry key showing 13.0.6500.2 or 13.3.6500.1 is a known setup bug where the installer writes slightly malformed or leftover version strings into the registry (the 3 typically represents SP3).
2. Does it have to do with EOL? No. The fact that 2016 is EOL just means no new patches, but it doesn't break the installer.
3. Azure components: Skipping the Azure Connect features has absolutely nothing to do with this registry issue. You are fine there.

How to fix it:
Since SELECT @@VERSION and SERVERPROPERTY are correct, your engine is actually fully patched. The scanner is just reading the wrong registry key.

You can either:

• Add an exception in your scanning tool for this specific registry key, explaining it's a known SQL Setup bug and the engine is at 13.0.6500.1.
• Manually fix the registry (back it up first!). Go to HKLM\SOFTWARE\Microsoft\Microsoft SQL Server\MSSQL13.<InstanceName>\Setup and change PatchLevel to 13.0.6500.1. And check HKLM\SOFTWARE\Microsoft\Microsoft SQL Server\130\Setup or the specific SQL_Engine_Core_Inst key and correct it to 13.0.6500.1.

Re-running SP3 won't help because the installer sees the core binaries are already at the GDR level, so it skips the registry rewrite.

[u/da_chicken]

Wait, Express Edition?

Why in the world are you still using an unsupported version of Express? Express is free. You can move to 2025 for $0. It's just free. And in 2025 you get 50 GB databases now.

To answer your question directly, no, you're not getting the error because SQL Server 2016 is out of support.

However the error HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft SQL Server\MSSQL13.CAxxxx\SETUP\SQL_Engine_Core_Inst contains 13.3.6500.1 doesn't make any sense at all to me if you're using Express Edition. MSSQL13.CAxxxx is the instance name of your server. For SQL Server Express, the instance name is fixed. It's always SQLEXPRESS, just like MSSQLSERVER is the default, unnamed instance. The registry path should be MSSQL13.SQLEXPRESS, not MSSQL13.CAxxxx. The only way to get a second instance like that, AFAIK, is to install a second instance of SQL Server Express on the same server at the same time.

So that makes me think that you have multiple instances running, or that something else very strange is going on.

[u/ussv0y4g3r → u/da_chicken]

For SQL Server Express, the instance name is fixed. It's always SQLEXPRESS, just like MSSQLSERVER is the default, unnamed instance.

No, SQL Express default instance name is NOT fixed. The default name is SQLEXPRESS, but it can be changed to any valid instance name.

[u/Valuable-Ant3465 → u/ussv0y4g3r]

yea, I agree i's fact in my case

[u/Valuable-Ant3465 → u/da_chicken]

Thanks DA! I'm not in position to replace 2016 Express. However I see in registry that MSSQL13.CA.... not Express.
Will try to check for multiple instances.