Hi Bruce. I'm seeing the exact same behavior as you reported. I have an application that exports data to a file geodatabase and then zips it up to make the database downloadable. The process replicates functionality from a desktop version of the application, so I can verify that the exact same code that works in desktop fails in server because a .freelist file is being held open in server (I suspect by an ArcSOC.exe service).
Have you had any success in solving this issue?
Thanks,
Brian
To bypass the locks that are placed on the file geodatabase by ArcGIS Server you should use a DeleteFeatures_management call followed by an Append_management call. The Copy_management tool copies the schema which is locked, but the schema is not touched when using DeleteFeatures_management followed by Append_management. I ran across this issue years ago and have used Delete and Append for years without any issues with file gdb locks.