If changes in the Geodatabase are necessary then all Esri ArcGIS Server Map Services based on the changed Geodatabase objects need to be stopped before (a running Map service or opened ArcMap document establishes a Geodatabase schema lock - no changes are possible).
Note: To assure that all changes in the Geodatabase take effect you should perform actions ‘Restart ArcGIS Server Object Manager (SOM)’ as well as ‘Restart Apache Tomcat service’.
Possible changes of the Geodatabase are
•Geodatabase alias definitions,
•Geodatabase structure (fields, field types),
•Esri domains, subtypes,
•etc.