This could be a noob problem but I couldn't find a solution so far. I'm developing a Rails app locally that uses SQLite, I've set up a local Git repo, and the dotcloud push command is using this. Locally I use the dev environment and on DotCloud it automatically uses the prod env, which is great. The problem is that each time I do a push my prod db on DotCloud gets lost, no matter how minor the changes are to the codebase, and I have to run 'rake db:migrate' to set it up again. I don't have a prod db locally, only the dev and test dbs.
The problem is that every time you deploy, the old version of your deployed app is wiped, and replaced with the new code, and your sqlite db is usually within your app files. I'm not a dotcloud user I don't know it it works, but you can try to setup a shared folder, where you put the production database on the server, which is outside of your rails app.