All I can say is what happened to me. I agree that it is odd behavior and seems unconnected, but I was looking at my decks and editing things one minute, I saw the new link and updated, and when I reloaded the plugin my decks were gone.
I delete the default decks whenever I update, and they always come back when i update. This was the first time they came back and essentially "replaced" my decks, though I assume it is just that my decks disappeared and the defaults came back, so replaced is the wrong word but you get what I mean.
I can also confirm that this occurred because I have lackey on dropbox in order to sync it across my computers. All of the decks showed as "deleted" at the same time stamp as when the default decks were shown as being created. That says to me that, indeed, the decks folder was modified by the update of the plugin.
Again, it doesn't really make sense to me, but this definitely happened one way or another, even if it somehow wasn't related to the update of the plugin. If it doesn't happen to anyone else, that's great news! But it MIGHT until someone can confirm what exactly about my setup caused the issue, which seems unlikely. So as a precaution, just making sure your deck folder is backed up right before you update seems safe, since this is such an unusual set of circumstances.
Hopefully it being in dropbox or something was the only issue, but whatever the case is, I would feel terrible if I didn't bring it up and save someone who doesn't have access to automatic backups a bunch of heartache.
Thanks for the new host and all the work everyone involved! Can't wait for fate reforged