First question, if there is something wrong with the SSD, then will my HDD be affected as well?
==> Possibly yes, if malware .... no, if SSD is broken or corrupted OS file on SSD. Since the HDD is merely a data drive, you might remove the SATA connector to keep anything from happening to it (like getting reformatted).
Regarding your question about booting from "one of these devices" I presume ur referring to an external harddrive?
==>HDD, flash drive, optical drive - some other device in or introduced to the system.. OK, need to clear the smoke...in post #3 you said " I chose Start-up Repair " - this indicates that you booted the system on something... was this the flash drive which you used before? or what?
To jump for a possible solution (which may NOT work), remove the HDD SATA connection, boot your installation media and do a custom clean install on SSD after removing old partition and putting in a new one with a reformat - and if that fails, download SSD diagnostics from SSD maker (which should be available if a major maker) and make a bootable diagnostic which can test the SSD and determine if you need to pursue warranty.
Otherwise, I need some more information:
system (maker, model) or is this DIY?
what OS you are using?
what is your warranty status?
what is the media you are using to boot & from what?
what error messages have you seen?
can you check SSD SMART in BIOS?