The repair program only works from within Windows so will only work on the drive that is booted up.
With just the affected drive installed, there are a couple of methods to get into the diagnostic mode which are where you boot up with the install media and select Repair your computer on the Install screen - Troubleshoot - Startup Repair or switch on then power shutdown when you see the Windows logo then do that another twice where the diagnostic mode will start for you to navigate to the same advanced options.
Using the latter method, if the Startup Repair reports that it is unable to auto repair your computer then click on Advanced options and select Command Prompt and enter chkdsk c: /f to see if that will repair the file structure.
That is more difficult if you've booted up with install media as it doesn't always see the volume as being in C:
Normally entering the cmd
bcdedit |find "osdevice" will give you the partition letter to use in the chkdsk cmd, but if it doesn't see the volume then it would be a guess as to which letter to use.
Mine can come up as D: or E:
For clarity, that is a Pipe symbol before find and is the uppercase of \
You can also check the status of the SSD with both drives installed by using the trial version of HDSentinel.
Download the Trial v5.30 (ZIP) version -
https://www.hdsentinel.com/download.phpUninstall when done which will stop the clock on the 30 day trial and then you can use it again as and when by reinstalling it from your Downloads folder.