I am reaching out to you guys for some help with a Derby indexing issue that we have run into at Monsanto, St. Louis. The issue is pretty much the same issue that was reported by Thomas J. Taylor in 2007 (The link is provided below).

Brief Description:
I have a database that was originally created with Derby and was
recently upgraded to Derby I've performed this upgrade on several
copies of the same database schema (each created on different computers,
but with the same version of Java (1.5.0_07) and Derby (10.1)).

For all but one of the database upgrades, it worked correctly. However, in
one case, it appears that the PRIMARY KEY and FOREIGN KEY constraints have
been lost/corrupted. When I use DBLook to check a 'working' database, I see
the appropriate constraints for keys. However, on the 'defective' database,
these constraints are missing.

We have over 80 tables in the DB and over 1000 users. Even though we have only 2 reported occurrences of this issue so far, it might be more widespread. It is a nightmare to manually identify the corrupted indexes for each occurrence. Any thoughts on how we can tackle this through a programmatic approach?

Here is the link to the old report: