The documentation currently does not address the need to upgrade databases in jars when connecting to a newer version of Derby.
For example, attempting to connect to a database in a jar created with Derby 10.0 fails when trying to connect with Derby 10.1. The following error is thrown:
ERROR XJ040: Failed to start database 'jar:(pathtojarfile)pathinjar', see the next exception for details.
ERROR 40XD1: Container was opened in read-only mode.