Scenario
Something in that database layer is broken, you want to clear all database tables and start fresh.
Backup your chosen profiles. All pre-existing JEMH configuration will be wiped with this process
Locate your license key that will be needed to enable JEMH.
Uninstall JEMH
Remove the JIRA_HOME/data/jemh folder entirely (this removes all history and test case content)
JEMH configuration database tables have names that start with AO_78C957. The below script contains the tables found in recent versions of JEMH. Modify the following drop script as required (some tables may not exist for you) - this is for SQLServer:
Table drop script for SQL Server
drop table dbo.AO_78C957_ALIASES drop table dbo.AO_78C957_AUDITCONF drop table dbo.AO_78C957_AUDITEVENTS drop table dbo.AO_78C957_AUDITHINT drop table dbo.AO_78C957_AUDITMETA drop table dbo.AO_78C957_AUDITMETA_DOMAIN drop table dbo.AO_78C957_AUDITMETA_PROJECT drop table dbo.AO_78C957_AUDIT_SUMMARY drop table dbo.AO_78C957_AUTOLABELCONF drop table dbo.AO_78C957_AUTOLABELIGNORE drop table dbo.AO_78C957_AUTOLABELSUBS drop table dbo.AO_78C957_BLACKLISTING drop table dbo.AO_78C957_CFDEFAULT drop table dbo.AO_78C957_COLONSUFXFPCONF drop table dbo.AO_78C957_CONFIG drop table dbo.AO_78C957_DIRSET drop table dbo.AO_78C957_DIRSETLINK drop table dbo.AO_78C957_EML_ADDR_TRCKR drop table dbo.AO_78C957_ENABLED_FEATURES drop table dbo.AO_78C957_ENABLED_MSG_FILTERS drop table dbo.AO_78C957_FEATURECONF drop table dbo.AO_78C957_FIELDPROC drop table dbo.AO_78C957_JEMHSYNC_EVENTS drop table dbo.AO_78C957_LDAPCONF drop table dbo.AO_78C957_LSNR_CONF drop table dbo.AO_78C957_LSNR_JPROJ_TMPL drop table dbo.AO_78C957_LSNR_PROJ drop table dbo.AO_78C957_LSNR_PROJ_TMPL drop table dbo.AO_78C957_LSNR_TRANPRJTMPL drop table dbo.AO_78C957_LSNR_TRANSPRT drop table dbo.AO_78C957_NAGCONFIG drop table dbo.AO_78C957_NAGPHRASE drop table dbo.AO_78C957_NAGPHRASESET drop table dbo.AO_78C957_NOTIFICATION_HIST drop table dbo.AO_78C957_PRE_PROC_TASK drop table dbo.AO_78C957_PRJDOMMAP drop table dbo.AO_78C957_PRJGRPMAP drop table dbo.AO_78C957_PRJKYWRDMAP drop table dbo.AO_78C957_PROFILE drop table dbo.AO_78C957_PROJCONFIG drop table dbo.AO_78C957_PROPERTY drop table dbo.AO_78C957_REGEXPPROCCNF drop table dbo.AO_78C957_REGEXPPROCMAP drop table dbo.AO_78C957_STATUS_NTFYCNF drop table dbo.AO_78C957_SUPPORT drop table dbo.AO_78C957_TEMPLATESET drop table dbo.AO_78C957_TESTCASE drop table dbo.AO_78C957_USEREVENTCNF drop table dbo.AO_78C957_USERSIGNUP drop table dbo.AO_78C957_WEBFORMCONF drop table dbo.AO_78C957_WEBFORMITEM drop table dbo.AO_78C957_WUFOOCONF drop table dbo.AO_78C957_WUFOOFORMFIELDS drop table dbo.AO_78C957_WUFOOFORMS
Restart JIRA
Reinstall JEMH
Install the license key
Restore your JEMH Profiles
Re-edit the inbound mail handlers that used JEMH Profiles, be sure to select the list item that is appropriate.
Oracle (and possibly other) databases
There are _SEQuences relating to the above that will also need to be dropped.