After an APS Package update, when a new package introduces CCP v2 support, a customer sees items from both old and new applications. For example, there are two tabs in MyCP, one for CCP v2 view, another with embedded CCP v1.
Both navigation trees are built basing on obsoleted information in applications' metadata cache.
The problem can be easily fixed by running the following command on all UI nodes except the Management Node:
# systemctl restart pau
on CentOS 6:
# service pau restart