Ah, well that was intentional. I tried using Windows to resize the partition first, after emptying the Recycle Bin and defragmenting (forgot about disabling special files though), but it wasn't able to reduce the partition size as much as I needed it to. I'll try the repair installation and see if it works. If not, then I can mount the Windows partition from Linux and copy any useful files to another partition, so I won't have to resort to data recovery.

Looking at it now, I see that a repair install can only be done from within Windows, so that doesn't help me.

You can do that using a Windows 7 SP1 DVD/USB. Details in the above article.

No, I can't. The article explicitly says (multiple times) that you need to be already running Windows to perform a repair install; besides, I tried it, and it won't let me use the Upgrade option when booting from a DVD.

Does Linux manage to mount the disk, and can you see the file-system and especially drill into the Windows folder and even copy files out of it? Can you boot the Windows DVD into DOS and see the disk? Try also to disconnect any possible device from the computer.

More: I still don't understand what goes wrong when you boot from the Windows 7 installation disc, follow the instructions to set the language, time and keyboard, click "Next", then select "Repair your computer" followed by "Startup Repair".

I can access any file on the Windows partition by mounting it under Linux - viewing, copying, deleting, editing - with no problems. (I haven't tried them all of course, but a representative sample yielded no errors.) I don't see a way to boot the DVD into DOS; can you point me to instructions? When I try Startup Repair I get the message "Startup Repair cannot repair this computer automatically".

I understand that repair lets you select the Windows partition, which is good. When you are notified it cannot repair, click "Don't send", go into the recovery/repair options, click "Command prompt" and enter the commands: bootrec /fixmbr and bootrec /fixboot, then follow with the instructions at the end of this article. It might also be a good idea to try chkdsk C: /r; run again adding /f if errors are found. Another to try is sfc /scannow. Add to the post the results for all these commands.

Actually repair doesn't let me select the Windows partition. Sorry not to make that clear. The screen where I would select a partition looks like this - no partitions listed - and I get to Startup Repair by just clicking "Next" anyway. I'll edit the question with this and also the output of bootrec.

Hey! Why does the Windows partition come up as D: ? What is C: ?

There's an NTFS data partition on drive #1 (an SSD), which the recovery environment maps to C:. (Of course when I was able to boot into Windows, the Windows system partition was C: and the data partition was E:.)

Please post the output of the DiskPart sub-command List Disk. Please also take out of the computer or disconnect all disks except the one you boot from. The disk must be recognized as C.

I've edited the question to include that output. As I noted there, the effects of all these commands appear to be the same (i.e. no effect) whether all drives are connected or not.

If you disconnect the drive #1, does the drive-letter change to C? Also, have you perhaps by chance inverted the connectors between disks #0 and #1 (when booting into the BIOS, are the disks in their correct slots)?

I've been using 1-based numbering, so there is no drive #0; anyway, yes, the drive letter does change to C when I disconnect drive #1. Throughout the whole process I've never disconnected drive #2 (the one the question is about), and I haven't changed which connector is attached to each drive, so there's no way the connectors are inverted.

There's still something wrong with your connectors. It may not be the only cause of the problem you are facing, but the boot drive must be the first slot in the BIOS or it doesn't get the C moniker. You probably made some changes over the years to your setup, but because this was done gradually things kept on working. Now you are faced with the need to redo it right. It would be best to reset the connections correctly and repeat the tests to see what will change.

Also: Note that a cheap way to reset Windows 7 boot is to partition empty space at the end of the disk and install Windows to it. This partition can be deleted later, but this sets up the boot correctly if nothing else will.

I did mention that I've run all the tests with all other drives disconnected, and it made no difference to the results.