Hello.
SCRIPT command has many flaws, but system sequences are going to be reimplemented together with identity columns when I or somebody else will find time to write a better implementation.
This command, however, is not designed for such use cases. You can use it, but you need to execute DROP ALL OBJECTS before RUNSCRIPT FROM, or you can delete your database, create a new empty one and execute RUNSCRIPT in it.
H2 has BACKUP command for online backups:
Backup can be restored by unpacking of archive (with offline database) or with Restore tool.