Welcome to the Digitalworldz UK PC Problems Forums, Discussing Strange HDD issue.

After replacing my atx case I decided to leave a 120GB HDD out and just use the 1TB one (which has the os installed on it). When I tried to boot up it gave me an error message "Ntldr missing". When I put the old HDD in and set the bios to boot from it it boots fine, but in windows there is nothing installed on it. Any ideas please as I'd like to get rid of it due to space issues thanks.

Did you check the wiring and can u
See drive in bios
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Looks to only occur on XP installs or where XP has previously been installed on another drive and a Vista/7 install detected the partition and the drive later removed.

The suggestion on the interwebs for those that can't get back into Windows is to use FixMBR etc via Recovery Console on the [F8] boot menu. That you can get back in to Windows you need to go to [WinKey]+[R] > diskmgmt.msc and change the active partition to the Win 7 install ([right click] > Mark Partition as Acticve). Personally I'd just back up your data and do a fresh install.

Thanks for that little pob, but now when I try to boot it without the 120GB in it say the MBR is missing

If you changed the active partition and are now getting the MBR missing message boot into recovery console (you'll need the 7 disc) and run /FixMBR: How to use the Bootrec.exe tool in the Windows Recovery Environment to troubleshoot and repair startup issues in Windows

you can install windows where the boot info is on 1 drive and windows directory etc is on another partition and or another drive this is easily done, i always disconnect any drives when i install win7 on a system even usb drives.

a useful free tool is easyBCD available here Download EasyBCD 2.1.2 - NeoSmart Technologies for free link is at bottom home use. you can see where every thing is with this util and move and repair.