MSSQL 2016 - Restore SSISDB from MSSQL 2012
I've ran into the same problem after restoring the SSISDB database from a lower SQL version to a higher SQL version; I've ran into:

SSIDDB Upgrade not working or erroring out on the &quot;sql version doesn't match&quot;
Validating packages erroring on customized_logging_levels not existing
all other errors one can encounter...

I noticed the newer SSISDB has more tables, views and different stored procedures. However there's a fairly easy solution, although unconventional.

restore the SSISDB on the &quot;new&quot; SQL (already Integration Services Catalog Enabled)
sp_changedbowner 'sa'
open master key decryption by password = 'yourkeyinserthere'
Alter Master Key Add encryption by Service Master Key
EXEC sp_change_users_login 'update_one', '##MS_SSISServerCleanupJobUser##','##MS_SSISServerCleanupJobLogin##'
ALTER DATABASE [SSISDB] SET COMPATIBILITY_LEVEL = 130 (or the one you need)
Install a CU higher then your current one

Installing the CU does the SSISDB upgrade and you can check that by looking at the table internal.catalog_properties. It will have a line &quot;upgrade from&quot;.
Also, what if you are already on the latest CU? Well, uninstall your last CU and reinstall it. That works too.