The fact that you boot from another hard drive should not cause data loss if acceleration is enabled. Acceleration will only work with the hard drive you choose in the Intel Rapid Storage Technology Software.
If you want you can disable acceleration before you install/boot from the other hard drive which is just for testing purposes. If the issue persists I recommend contacting HP in order to get more advanced troubleshooting steps. You can use this link http://www8.hp.com/us/en/contact-hp/contact.html