To ensure that everything is switched over to the new datasource, delete the deploy/hsqldb-ds.xml file and start JBoss. If it throws any errors, you missed a configuration file somewhere.
Overall, I've found that developing with the built-in Hypersonic database is less painful than having to manage an external database. However, in a production environment, Hypersonic is ill-suited to the task. Connecting JBoss to a more robust database goes a long way toward maintaining the performance of the server.