When backing up a Windows Server 2012 R2 instance with Rapid Recovery, the ThinkAgile CP service should be stopped before taking a backup.
To automate this process, you can use Rapid Recovery pre- and post-transfer scripts as described in the following website:
Quest Rapid Recovery Commands and Scripting Reference Guide
On the 2012 R2 agent, open notepad and enter Stop-Service tacp; and save the file as C:\Users\All Users\AppRecovery\Scripts\PreTransferScript.ps1
On the 2012 R2 agent, open notepad and enter Start-Service tacp; and save the file as C:\Users\All Users\AppRecovery\Scripts\PostTransferScript.ps1