At Yahoo we drop columns from the previous version the next time we upgrade the database, e.g. if you stopped using a 1.0 column in version 1.1, then you drop t

At Yahoo we drop columns from the previous version the next time we upgrade the database, e.g. if you stopped using a 1.0 column in version 1.1, then you drop that column as part of the upgrade going to 1.2. The key thing is always being able to roll back if things go seriously wrong; hardware is much, much cheaper than downtime.