Have you tried doing an integrity check on the database file?
I've had to "recover" a Banshee library that was corrupted in the past -
all of the data was still there, but some of the indices were broken. I
solved the problem by backing up the database, creating a new database
with the same schema, and then restoring the data. This rebuilt the
indices without having to re-import all of the data.
Check out this article for more info:
http://thelinuxexperiment.com/guinea-pigs/jon-f/recovering-a-corrupted-banshee-database/
Best of luck!
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Jonathan Fritz
On the Web:
http://www.jonathanfritz.ca