Spare hard disk prevents windows loading

I have W7 installed on a 1TB disk, and a spare 3TB disk.

I'm trying to change the OS from the 1TB disk to the 3TB disk.

I used a partitioning program to change the 3TB disk's FAT partition to NTFS, (thinking it would improve performance!)

Now, if the 3TB disk is connected, none of the operating systems (that is the W7 on the 1TB disk, nor the W7 installation CD disk) will start. I get the message "loading Operating system", then .....nothing.

I use the F12 key which should allow me to choose which disk to use. I have also used BIOS setup to set the disk I need.

To summarise, I can only start Windows by disconnecting the 3TB disk, I therefore can't access the 3TB disk at all.

Have I made the 3TB disk unuseable?

Any advice would be very much appreciated.