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Realcase: Failed to upgrade SQL Server 2016 SP2 CU11. (Installation success or error status: 1648)

One of my customer failed to upgrade SQL Server 2016 SP2 CU11.
Here is the troubleshooting steps

1.Check SQL Server setup log(C:\Program Files\Microsoft SQL Server\130\Setup Bootstrap\Log\)

Detailed results:
  Feature:                       Database Engine Services
  Status:                        Failed: see logs for details
  Reason for failure:            An error occurred for a dependency of the feature causing the setup process for the feature to fail.
  Next Step:                     Use the following information to resolve the error, and then try the setup process again.
  Component name:                SQL Server Common Files
  Component error code:          1648
  Component log file:            C:\Program Files\Microsoft SQL Server\130\Setup Bootstrap\Log\20191217_193009\SQLAG\sql_common_core_Cpu64_1.log
  Error description:             No valid sequence could be found for the set of updates.
  Error help link:               http://go.microsoft.com/fwlink?LinkId=20476&ProdName=Microsoft+SQL+Server&EvtSrc=setup.rll&EvtID=50000&ProdVer=13.0.5337.0&EvtType=sql_common_core.msi%400x162A16FE%400x1648

2.Reviewed the File sql_common_core_Cpu64_1.log

MSI (s) (78:C0) [19:43:48:678]: APPCOMPAT: looking for appcompat database entry with ProductCode '{57846DA8-8B5D-4466-B850-E8CDFC94046C}'.
MSI (s) (78:C0) [19:43:48:678]: APPCOMPAT: no matching ProductCode found in database.
MSI (s) (78:C0) [19:43:48:678]: Opening existing patch 'c:\windows\Installer\583222d.msp'.
MSI (s) (78:C0) [19:43:48:694]: Note: 1: 2205 2:  3: MsiPatchSequence 
MSI (s) (78:C0) [19:43:48:694]: Opening existing patch 'C:\windows\Installer\1540d9.msp'.
MSI (s) (78:C0) [19:43:48:694]: Note: 1: 1402 2: HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Policies\Explorer 3: 2 
MSI (s) (78:C0) [19:43:48:694]: File will have security applied from OpCode.
MSI (s) (78:C0) [19:43:49:960]: Original patch ==> C:\sp2\x64\setup\sql_common_core_msi\sql_common_core.msp
MSI (s) (78:C0) [19:43:49:960]: Patch we're running from ==> C:\windows\Installer\583222d.msp
MSI (s) (78:C0) [19:43:49:960]: SOFTWARE RESTRICTION POLICY: Verifying patch --> 'C:\sp2\x64\setup\sql_common_core_msi\sql_common_core.msp' against software restriction policy
MSI (s) (78:C0) [19:43:49:960]: SOFTWARE RESTRICTION POLICY: C:\sp2\x64\setup\sql_common_core_msi\sql_common_core.msp has a digital signature
MSI (s) (78:C0) [19:43:50:007]: SOFTWARE RESTRICTION POLICY: C:\sp2\x64\setup\sql_common_core_msi\sql_common_core.msp is permitted to run at the 'unrestricted' authorization level.
MSI (s) (78:C0) [19:43:50:007]: SequencePatches starts. Product code: {57846DA8-8B5D-4466-B850-E8CDFC94046C}, Product version: 13.0.1601.5, Upgrade code: {F2F6463E-EE2A-4C0B-B399-F550C887354A}, Product language 1033
MSI (s) (78:C0) [19:43:50:007]: Note: 1: 2205 2:  3: MsiPatchSequence 
MSI (s) (78:C0) [19:43:50:007]: Note: 1: 2203 2: RTM.1 3: -2147287038 
MSI (s) (78:C0) [19:43:50:007]: PATCH SEQUENCER ERROR: failed to open RTM.1 transform in {DC33A855-F84A-4772-95CB-1C47EFE27DAD} patch! (1: 2203 2: RTM.1 3: -2147287038 )
MSI (s) (78:C0) [19:43:50:007]: SequencePatches returns error 1648.
MSI (s) (78:C0) [19:43:50:007]: Product: SQL Server 2016 Common Files - Update '{947AECBA-66AD-4F92-A153-7192D8C27963}' could not be installed. Error code 1648. Additional information is available in the log file C:\Program Files\Microsoft SQL Server\130\Setup Bootstrap\Log\20191217_193009\SQLAG\sql_common_core_Cpu64_1.log.

MSI (s) (78:C0) [19:43:50:007]: Windows Installer installed an update. Product Name: SQL Server 2016 Common Files. Product Version: 13.0.1601.5. Product Language: 1033. Manufacturer: Microsoft Corporation. Update Name: {947AECBA-66AD-4F92-A153-7192D8C27963}. Installation success or error status: 1648.

MSI (s) (78:C0) [19:43:50:007]: Note: 1: 1708 
MSI (s) (78:C0) [19:43:50:007]: Product: SQL Server 2016 Common Files -- Installation failed.

MSI (s) (78:C0) [19:43:50:007]: Windows Installer installed the product. Product Name: SQL Server 2016 Common Files. Product Version: 13.0.1601.5. Product Language: 1033. Manufacturer: Microsoft Corporation. Installation success or error status: 1648.

MSI (s) (78:C0) [19:43:50:007]: Attempting to delete file C:\windows\Installer\5c2971d.msp
MSI (s) (78:C0) [19:43:50:007]: MainEngineThread is returning 1648
MSI (s) (78:44) [19:43:50:007]: No System Restore sequence number for this installation.
No valid sequence could be found for the set of updates.

3.Here is how SQL Server upgraded to CU11 for sql_common_core.msp:
1)It runs the file of sql_common_core.msp of each patch.
In this case, it has two version of sql_common_core.msp ,SQL Server 2016 SP1 and SQL Server 2016 SP2.
2)’c:\windows\Installer\583222d.msp’ is for SQL Server 2016 SP2 and ‘C:\windows\Installer\1540d9.msp’ is for SQL Server 2016 SP1.

3)It failed to run 583222d.msp and caused entire upgrading fail.

The following screenshot is how I find the real names of two files. Please read this article for more detail.

image

4.I RDP to the SQL Server windows server, I found that something strange:
The size of is only 20KB, which is abnormal.

image
5.I download the SQL Server 2016 SP2 and compared, the correct size is around 4.7MB.
6.Then I replaced the invalid the file with the file I extracted from SP2.
7.Tried the installation and it worked.

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