Can't Remove Empty Hard Drive

I'm a photographer with 3 old-tower-based PCs that I look after myself, all with Win7 and SATA2 disks. Naturally, I need ever-larger storage space. To that end I moved all the data from a 1Tb disk to a 2Tb disk, then removed the 1Tb disk intending to replace it with a 3Tb disk. However, without the 1Tb disk, this PC would not boot, and the repair disk couldn't locate any Windows OS. But the OS is on another disk entirely (that remained connected throughout all this). I re-connected the 1Tb disk and the PC booted just fine. On inspection I find that this 1Tb disk - that I thought was entirely empty - has on it a 100MB System Reserved Partition that might relate to the MS back-up system that I've never used (as Win7 seems to point to this, although telling me it's not big enough to use for a backup!) By assigning a letter to this 100MB partition, I can see that there's a handful of (normally hidden) files and a directory relating to booting the PC. I therefore conclude that the PC is booting from this partition on the 1Tb disk, even though the OS is on a separate disk. How do I get the PC to boot from the 'OS' disk so that I can exchange the offending 1Tb drive with a 3Tb one? Or is there some other solution? Maybe I just copy this partition to the new disk? (BTW, I've already registered the 3Tb disk on the system.