Hi Zubai,
When you reboot the Central Manager, you must re-enable secure store encryption manually. Disk encryption and CIFS preposition features on the remote WAE devices will not operate properly until you enter the secure store password on the Central Manager to re-enable secure store encryption.
Please refer to the following document for more detail about re-initializing the secure store:
http://www.cisco.com/en/US/docs/app_ntwk_services/waas/waas/v413/configuration/guide/other.html#wp1053890
Best regards,
Ahmad