Once the container hosting plan is updated to the latest then all applications are reinstalled again.
Action log indicates that all applications are removed and then installed into the container back. For example:
Top > Configuration Director > Logging and Errors > Action Log
2395886 OK Success #4446 container.tld; #837 SpamAssassin 3.2.3-2 Install an application into the Container; Installing templates into container.tld 2395854 OK Success #4446 container.tld; #837 SpamAssassin 3.2.3-2 Remove an application from the Container; Removing templates from container.tld
The issue appears for Standard Virtuozzo Templates only. This is caused by the new functionality implemented since PBA-S 4.2:
(03) Features added: 16 ... 8 Multiple OS Templates Selection for PVC Hosting Plan It's now possible to make several operating systems available for a PVC hosting plan.
Hosting Plan assigned to subscription #4446 container.tld includes several OS Templates:
Top > Billing Director > Product Manager > Hosting Plans > %plan_name% > OS Templates
CentOS 4.5 p8. CentOS 4.2 p2. CentOS 4.2 p6. CentOS 4.2 p7.
This causes Standard Applications Templates are reinstalled during container synchronization.
To avoid the application removal on each container synchronization if hosting plan includes another version of OS template, it is recommended to switch to EZ templates:
http://www.parallels.com/fileadmin/parallels/documents/hosting-cloud-enablement/pvc/pvc_updates/VzLinuxTmplMgmt.pdf (page 75).