"Schema contains no tables." after 2026.1.3 upgrade

Upgrading from 2023.11.4 to 2026.1.3 using MSSQL database. The original installation was fully working. After upgrade, the database connection succeeds, but reports no tables exist and startup fails.

I have confirmed that the database remains intact, with the latest database version noted in the db_version table as 1003.

The relevant log section:

[2026-07-29 13:58:31,577]   INFO -  jetbrains.buildServer.STARTUP - TeamCity main node (id: MAIN_SERVER) is starting...
[2026-07-29 13:58:31,636]   INFO - er.https.HttpsConfiguratorImpl - Https is not configured.
[2026-07-29 13:58:31,675]   INFO -  jetbrains.buildServer.STARTUP - Current stage: Looking for the database configuration
[2026-07-29 13:58:31,676]   INFO -  jetbrains.buildServer.STARTUP - Database properties file "F:\TeamCityData\config\database.properties" exists
[2026-07-29 13:58:31,677]   INFO -  jetbrains.buildServer.STARTUP - Internal HSQL database file (F:\TeamCityData\system\buildserver.data) doesn't exist
[2026-07-29 13:58:31,677]   INFO -  jetbrains.buildServer.STARTUP - Database connection URL: jdbc:sqlserver://redacted:1433;databaseName=TeamCity;integratedSecurity=true
[2026-07-29 13:58:31,683]   INFO -  jetbrains.buildServer.STARTUP - Using external (MSSQL) database
[2026-07-29 13:58:31,683]   INFO -  jetbrains.buildServer.STARTUP - Current stage: Connecting to the database
[2026-07-29 13:58:31,693]   INFO -  jetbrains.buildServer.STARTUP - JDBC loader: loading JDBC drivers (for the first time)
[2026-07-29 13:58:32,044]   INFO -  jetbrains.buildServer.STARTUP - Effective database connection properties:
[2026-07-29 13:58:32,045]   INFO -  jetbrains.buildServer.STARTUP -     applicationName=TeamCity [defaults]
[2026-07-29 13:58:32,045]   INFO -  jetbrains.buildServer.STARTUP -     encrypt=true [connectionProperties.*]
[2026-07-29 13:58:32,045]   INFO -  jetbrains.buildServer.STARTUP -     sendStringParametersAsUnicode=false [defaults]
[2026-07-29 13:58:32,046]   INFO -  jetbrains.buildServer.STARTUP -     trustServerCertificate=true [connectionProperties.*]
[2026-07-29 13:58:33,193]   INFO -  jetbrains.buildServer.STARTUP - Native library mssql-jdbc_auth-12.6.5.x64.dll was found under F:\TeamCityData\system\caches\jdbc\native\windows-amd64.
[2026-07-29 13:58:33,899]   INFO -  jetbrains.buildServer.STARTUP - Database character set: SQL_Latin1_General_CP1
[2026-07-29 13:58:33,899]   INFO -  jetbrains.buildServer.STARTUP - Database collation: SQL_Latin1_General_CP1_CI_AS
[2026-07-29 13:58:34,150]   INFO -  jetbrains.buildServer.STARTUP - JDBC driver version: 12.6 (Microsoft JDBC Driver 12.6 for SQL Server)
[2026-07-29 13:58:34,150]   INFO -  jetbrains.buildServer.STARTUP - Database system version: 13.0.7085 (Microsoft SQL Server)
[2026-07-29 13:58:34,150]   INFO -  jetbrains.buildServer.STARTUP - Connected to the database successfully
[2026-07-29 13:58:34,150]   INFO -  jetbrains.buildServer.STARTUP - Current stage: Checking the database
[2026-07-29 13:58:34,545]   INFO -  jetbrains.buildServer.STARTUP - Using schema: 
[2026-07-29 13:58:34,561]   INFO -  jetbrains.buildServer.STARTUP - Schema contains no tables.
[2026-07-29 13:58:34,576]  ERROR -  jetbrains.buildServer.STARTUP - Data parts are inconsistent: the Data Directory exists (from another version of TeamCity) but the database does not.
[2026-07-29 13:58:34,576]   INFO -  jetbrains.buildServer.STARTUP - Current stage: TeamCity server startup error
[2026-07-29 13:58:34,576]   INFO -  jetbrains.buildServer.STARTUP - Administrator can login from web UI using super user authentication token (better use a private browser window)
 

I have also tried with the updated JDBC