Deleting projects that have a big number of issues takes some time and causes timeouts in OnDemand. Result: an electric charlie or a "Page unavailable" error screen. As a result, indexes for the deleted project stay in place, and it's still visible under JIRA Admin > Projects. Another attempt to delete it results in an error:

Exception removing project: Error removing issues: java.lang.NullPointerException

Workaround: fully reindex JIRA to remove traces of the deleted project (background reindexing times out in the UI, and doesn't remove the deleted project).