those are the two the one that have patch note. The other have some change modification to the file, who know what include. I would probably wait a few days till the update seem to stop.
Tried to wipe my save & I still have that endgame freeze I have above. Other also seem to have other bugs.
Just so you know, those two "updates" I mentioned, so essentially the Steam patch notes, actually translate to changes in the game files - I mean, how WOULDN'T they? And yes, most likely to the file 'CommonEvents.json'...
I mean the last build "change", on the 20th, according to the above linked steamdb page, has OP.mp4 added to the download in the movies directory. That probably doesn't have anything to do with your error, now does it? I mean, like 99,99% doesn't (...well, 100%).
Anyhow, I would defo start by not running the game from the desktop. Not a good practice, most of the time. Put it in C:\Games\Shinobi or something.
If not that... You will probably need a relevant bugfix, indeed.