If the license is registered to that system changing the hard drive and reinstalling the SAME version of windows won’t be an issue. MS saves your system’s “fingerprint” and as long as you don’t change too many parts, it will recognize it and attach the license back to it.

If you do lose the license on reinstall, there are site that will sell you a cheap license, buyer beware, or ultimately you could switch over to something like truenas (core or scale) to run plex which is license free.

All drives will ultimately fail, could be 10years, could be 10mins. If you don’t want to lose your data, back it up. Have a storage drive and a backup drive. Don’t both connected them to the router. Use an alternative method to connect , like to a computer and have run a backup protocol on a regular basis. As for 2.5 over 3.5, the 3.5 are usually faster but it probably doesn’t matter reliability wise.

I would second the bad disk. I thought bad permission but since since it seems intermittent, the bad disk is the better guess. It would be good to get more info like what’s it running on, is it an array, etc.