Good day! I'm Dhanam a Windows user like you and I'll be happy to assist you today. I know this has been difficult for you, Rest assured, I'm going to do my best to help you.
Normally, If you delete the System32 folder, your computer will have the following problems: No longer be able to start up. This is because many critical system files are stored in that folder. Without those files, your computer won't be able to boot up properly.
But if you delete system32 folder in non-OS SSD( you must boot Windows from Other SSD) it won't make any difference, You won't start Windows ( from Win32 deleted SSD) in future for any issue.
I hope this helps. If this is not exactly what you need, please explain more so that I can help you better.
Regards
Dhanam