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1. Add SkyrimSE.exe, SKSE64_Loader.exe, and Steam as exceptions to Windows Defender.
2. Be sure you have Steam open before using SKSE.
I'm on mobile and can't do a lot of research. Alex may be along to help.
I wonder what is meant by "the runtime".
"Remove the files from Data/SKSE/Plugins and try again. Mods using plugins probably need to be updated. Before contacting us, make sure that your game launches properly without SKSE first."- silverlock.org (SKSE main website).
Hope it helps.
You may be seeing a blue update button and was trying to setup an older modded version to keep an old modded save alive, as you mentioned.
As you have noted, a clean reinstall of the current version may be needed if you don't have a full backup of the entire game folder you could use.
I recommend keeping the latest version for modding unless there is an old mod you can't live without.
Once some mods update to 1179 (e.g., Simply Knock), I will change how I back it all up. At the moment I have been packing the game files and mod files in the same 7zip archive (separate folders with relative filepaths in MO2) and it always worked so far by extracting the lot onto a non-C disk. But for a completely new Windows install, I should have kept the install packages and the mod files in separate archives for the game to be installed correctly while the mods can still simply be extracted.
I have a copy of the vanilla game (v. 1.6.640) made a year ago when I performed a clean reinstall. I made a full copy of the game folder as well as having a couple of backups of my modded game that are about a month apart. This totals about 170GB. Hard drive space is cheap right now.
It is very handy for Steam users as I could update the game to 1.6.11[3,7]0, delete the entire folder when complete, and then copy in the backup. This allowed me to change the blue update button back to green when it got annoying to look at.