No. It's just a patch. It's got nothing to do with your save. I first downloaded it after installing it on hshop, too. The intro FMV still has the same subtitles from the Google translate version if you do it that way, though. I uninstalled it, and reinstalled it again to get rid of it, because I didn't like it. Obviously, that DOES affect your save, but you could always back up with Checkpoint or JK's save editor.
I think this new translation is basically a big DLC. I've installed atop of the google-translated version and every was great, finished the game properly. When I was done with the story I deleted said 'DLC' and the game returned to old translation, which is enough for endgame, but got a lot of SD space freed.
A VPN won't protect you from a virus either way. That's not what a VPN does.
Does Spotpass matter? I've searched around and saw that there are Spotpass DLCs. And so far haven't been able to download them after enabling Spotpass in-game.
We have some save files on the Discord that have the SpotPass missions enabled.
