I understand the Intel® Rapid Storage Technology is automatically assigning the new drive to the RAID Array_0000 instead of the Array_0001.
This is an expected behavior since the software does not have the option yet to select what array do you want to fix. Since you have two arrays, the Intel® Rapid Storage Technology automatically will start rebuilding the first one.
Since you have RAID 1 configured in your system, the best and easiest option is to Access CTRL+I and set the Disks from array_0001 to non RAID. When you do this, the Option ROM will display a generic alert that says “All information will be lost”; however, this does not apply for RAID 1.
So by setting up the Disks from Array_0001 to non RAID disk, you will keep all the information in the HDD. Once done this, you may access the operating system and open the Intel® Rapid Storage Technology and from the Create tab you have the possibility to create a RAID from the selected disk and you also will have the chance to select the new disk and create the RAID Array from there.
You can get the Intel® Rapid Storage Technology user guide at the following link: