For Agents, Viewer and Change Assistant:

Delete the following directories, under PS_HOME\PSEMAgent for Agents, under PS_HOME\PSEMViewer for the Viewer and under the Change Assistant directory for Change Assistant.

envmetadata/PersistentStorage
envmetadata/scratchpad
envmetadata/data/ids
envmetadata/transactions (if it exists)

For Agents and Change Assistant delete the following file:

envmetadata/data/search-results.xml

For HUB

Delete the following directories under PS_HOME\webserv\peoplesoft\applications\peoplesoft\PSEMHUB
if your domain name is not 'peoplesoft' then change the above directory accordingly.

PSEMHUB\envmetadata\Scratchpad
PSEMHUB\envmetadata\PersistentStorage
PSEMHUB\envmetadata\transactions (if it exists)

Also delete all files and directories within:
PSEMHUB\envmetadata\data\*.* (files and directories.don't delete the data directory itself)