How to reinstall external Hdd drives?

That's bad cloning a disk with bad sector will write those to the new drive. If there were bad sector windows may be corrupted which could be the problem. What do the disk show in disk management. Try booting from a live cd lots of free ones and see if they see the drives if they do then windows is corrupted

If you cloned a bad drive (presumably a forensic clone, as a decent cloning program wouldn't let you clone a partition with bad sectors) then it's quite possible that your 'new' system disk (I assume you're referring to cloning your system disk) contains errors if the bad sectors on the old one corrupted system files.

It all depends how many bad sectors there were, and any file corruption arose from that.

I'm going to guess you found there were problems with your O/S, checked the disk, found bad sectors were reported, then cloned it.

Do you know how you could have protected yourself properly?
By using 3rd party disk imaging regularly and routinely.
If you had an image created before this occurred you could have restored that.

This is how/whay that could have helped you:

Example- one time I next imaged a disk in my PC using Macrium Reflect, there was a CRC error during the imaging procedure.
I checked the disk- some bad sectors- the disk was beginning to fail.
I don't know if other imaging programs do that check- but that's what saved me and gave me early warning.

As for running SFC /SCANNOW - it's not clear from what you say whether that passed or not.

It sounds like you have a randomly damaged O/S - whether it's possible to do anything with it is uncertain.

Try:
a. From an admin command prompt run
chdsk c: /scan
- scans only
Look at the last few lines- check it's passed.

b. Similarly run
SFC /SCANNOW
Look at the last few lines- check it's passed.

Now try an in-place upgrade repair install which keeps all progs and data

Tutorial available - in the searchable Tutorials section.

Who knows? You might get lucky.

(You don't 'reinstall external drives' - you should just connect them, and they should be recognised...).

I usually open File Explorer, go to the drive then to Properties then to Tools and run Error Checking. SFC [System File Check] is for,,,,,,,,the Operating System files.

Out of curiosity, exactly how did you clone it? I.e. did you intentionally use a tool that ignored bad sectors, or do a so-called 'forensic' clone... or put another way, which cloning tool should be avoided if you didn't opt to do that, and yet got no warning?

And how bad were the bad sectors, if you see what I mean... e.g. a marginal SMART check failure, or a massive failure?

Did you boot a live cd to try drives as that proves windows is corrupted if they work. Any bad sector you don't know what is corrupted clean install is best solution

You need to prepare for a clean install. Consider e.g. browser-related data- favourites, passwords maybe? Program license codes.. . email client-related data if you use one.. anything that may be hard to retrieve offline.

As soon as you have a working system, start using sound backup practices.
Use disk imaging (to an external drive)- start as early as you can and repeat throughout the process of installing and configuring. Don't leave it too late- ensure you lose the least work if something goes wrong.

You can set Crystal Diskinfo (free) to monitor your disk(s) state and alert you to degradation against preset thresholds.

Again - what did you use to do the clone?