When, the configurationcontext table contain entry associated to non-existing project, there are multiple Issue Types Schemes that is set as default. In addition to that, JIRA throws nullpointer exception when user navigate to the Project's Issue Type tab:

http-8282-3 ERROR jadmin 922x258x1 ws5lk 127.0.0.1 /plugins/servlet/project-config/ATL/summary [jira.projectconfig.contextproviders.SummaryContextProvider] Unable to load project summary panel
java.lang.NullPointerException
	at com.atlassian.jira.issue.fields.config.manager.IssueTypeSchemeManagerImpl.getIssueTypesForConfigScheme(IssueTypeSchemeManagerImpl.java:276)

The following SQL will shows the entry related to non-existing projects:

select * from configurationcontext where project not in (select id from project);

JIRA should ignore missing projects when using the configurationcontext.

Resolution

See this KB article:
https://confluence.atlassian.com/display/JIRAKB/JIRA+Throws+NullPointerException+When+Navigate+To+Project's+Issue+Types+Tab