It depends on which partition the bootloader is stored on. Of course, the first part of the bootloader is stored in the MBR, which is not part of any partition, but the rest of it is just a regular executable on some partition. The program in the MBR just reads that executable into memory and runs it. Now, since you have two Windows installations, it's probably the case that each of them has a bootloader, but only one of the two actually gets used. If it's the one on the 64-bit Windows partition that is getting used, you should be able to format the 32-bit Windows partition without a problem. But if the bootloader on the 32-bit Windows partition is being used, you should probably switch that. To do so, I think you could put in your Windows installation disc (the 64-bit one) and there should be a Startup Repair option, or something like that, which you can use. Alternatively you could just format the 32-bit Windows partition, and if the system doesn't boot up afterwards, just stick in the 64-bit installation disc and use that Startup Repair - it should identify the problem and fix it.
By the way, formatting the partition won't remove the 32-bit Windows entry from the bootloader menu. Obviously that entry won't work any more, since if you selected it you'd be trying to boot from an empty partition, so you'd probably want to remove it. amphetamachine's answer describes how to do that.