Unable to repair BCD in Windows 7 (UEFI) thru Install disk

I have 3 hard disks . Windows 7 and Linux Mint is installed in 2 separate disks.

The problem started when a black screen with only mouse pointer started irritating me at boot. On shaking the mouse or After waiting for a few seconds however my windows would boot up .I ran sfc /scannow and found some corrupted files could not be repaired. I booted Installation media and ran startup repair which corrupted my BCD store. Now whenever I boot I get a PC recovery screen saying BCD is either missing or not bootable.

Now when I boot install media of Win 7 (UEFI mode)- USB , my Windows disk is not displayed in the box where it shows the current installation . Also The Fat 32 EFI boot folder (500 MB) is in Disk 2 and not in Win Hard drive.

I tried Hiren boot CD but the mini xp environment could not be booted as the video driver seems to be incompatible and only lines are appearing.

Since it is UEFI mode , pressing F8 at the time of Windows boot to log into safe mode is not working as on selection of Windows option immediately the error screen throws up.

is there any other utility I can run from a USB/DVD to repair the win partition? or can Mint do something? Upon googling I came across a utility called Lazesoft but its a Limited use trial version and I dont want to go with it .

Can I use Ultimate Boot CD (UBCD) on EFI?.

I am also hesitant to use MBR fix tools as I fear they may not work with UEFI firmware.

Why is your EFI System partition not on the same hard drive as Win7? You must have known this is not correct so why did you allow it to continue?

To repair the Win7 hard drive you need to unplug all other hard drives, but if you have the EFI partition on a separate hard drive then you need to include it.

See if you can rebuild the BCD from Step 5 of Troubleshooting Windows 7 Failure to Start.

Thanks I managed to Fix it ... I booted the install disk and used diskpart command to mount the EFI volume. Then I had to manually enter bcdedit commands to recreate the BCD store. (I got the commands from Windows OS Hub | IT knowledge base for system administrators) . After that I booted the install media .This time my win partition showed up (probably because I had redfined the win partition as OS partition in one of the commands) . I ran startup repair .. As usual it ran for a long time and upon reboot there was one improvement in that the windows logo appeared halfway and restarted after the 2 dots in the logo appeared. I was still unable to boot no matter how many times I ran the startup repair.

Finally I tried to see if some restore image was saved and luckily there were a couple of snapshots. I chose one of them and the system restored the files.

Now I am again able to boot into windows!

Please post back a screenshot of Disk Management - Post a Screen Capture Image
so we can look over your configuration now.

Thanks Greg! Sorry for the delayed reply. I was kinda busy at office. I fully understand my folly now

At the time of installation , Non Windows disk was given the first priority in BIOS (2 disk in which Linux is installed). THough clean install was done on a blank disk , the EFI (boot) partition got installed in the 2nd disk. So now my partition is as follows:

1. Disk 1 - (250GB) - (a) 500 MB FAT32 (EFI) (b) 37 GB Ext 4 Linux home (c) Linux swap - 2GB Bal free
2. Disk 2- Win partition (1TB) - (a) Windows system - 40 GB (b) balance free
3. Disk 3 - Win Data (320 GB) -(a) NTFS completely for Storage

(sorry did not have the time to post screen shot )

I have also read your reply in one of the other post wherein you have guided someone on how to move the EFI partition to win part

1. Install Macrium reflector
2. Create image of Win and EFI part
3. From bootable disk , delete win partition
4. Restore both EFI and WIn to the deleted partition
5. Change BIOS boot order and mark only the win with boot flag and active
6. Try startup repair
7. If it doesnt work change the boot order back to the EFI disk in BIOS to restore earlier position

I got the idea , is there any way a partition can be pushed to the right to leave empty space in the left side of the block . Thought this would save the time of imaging , deleting and restoring (which seems to be risky ) . In most of the utils shrinking is always from end and you can add new part only to the right.

Think it is impossible but anyway thought would post this dumb qn with a faint possibility of some unknown utility which can do this

I stumbled upon this discovery wen I wanted to run SFC /SCANNOW to fix blackscreen with mouse problem , then only I realized fix is possible only when the boot and the Win are in the same disk.

Had windows given some warning that the boot (efi) is going to be in Non Win disk , I could have sorted the issue then and there.