Recovery steps for corrupted but bootable OS

[tns1]

What a bonehead move. I had an old reliable W7p system that I decided to move to W10p. To avoid messing with the W7 install, I used a 2nd older (but trouble free) HD to install W10. The install went fine, and both drives passed all the SFC, DISM, chkdsk tests I threw at them without showing any problems. At that point I put both drives in the system to more easily copy over user files.

Everytime I booted with both drives active the system would initiate a disk check for both drives, but no errors were found and it would finally boot whichever HD I had selected at the time - until it didn't. At the first sign of trouble I pulled the W10 HD and just booted to W7. The bootup disk check now showed dozens of index repairs/file recovery before W7 finally booted, and SFC and DISM cannot fix the issues. Restore points have all been lost. SMART data shows 20k hrs of use, but no failures of any kind.

The bonehead part is my last Macrium image of that HD is a year old. I was able to copy off all of the user files/folders in advance of any image restore or OS repair. Even so there are some recent installs/tweaks I'd rather not lose if I could. What steps such as a startup repair should I attempt in what order to best recover this drive before I resort to an image restore?

Note: So far none of my user files were harmed and many apps run without problems, but some system utils no longer work such as event viewer and disk manager. Oddly my email client works but my browser can't connect. My loss of restore points may be due to overzealous cleanup. When I first booted with both drives in the system, I noticed it had assigned drive letters on both drives to the normally hidden partitions (sys reserved, etc), and I used disk manager to remove those letter assignments. Was that a mistake?

 

[tns1]

I went with the image restore since a system repair would probably require just as much cleanup without any guarantee of success. After copying back my user files I made current images of the cleaned up W7, W10 disks. Still wondering what caused my W7 disk to get corrupted.

 

[samuria]

The resone you get disk check is because the dirty bit is set not because the disk is bad when windows starts up it writes a diry bit to the hd when it shuts down it clears it if it doesnt shut down correct the dirty bit stays which start disk check Dirty Bit: What Is It & How to Set/Clear/Reset It - MiniTool Partition Wizard

 

[tns1]

It is possible that I didn't have the SATA cable seated properly on one of the disks, but that really only accounts for a single bootup, not the dozen or so times I was getting the disk check. Every other time I know the machine was shutdown properly, yet the dirty bit seemed to be perpetually set on both drives. I was swapping the drives in and out of the PC in different slots, but I have done similar before and don't remember the disk check triggering every time.

 

[samuria]

Is the dirty bit still set?

 

[tns1]

I no longer get a disk check at boot, so if this is a reliable indicator then the dirty bit is not set.