I think I need to clarify a few things here.
We are not talking about reimporting the downloaded save into the online save again.
That is not true.
The GameJolt save is stored on the server entirely. Download an online save would download just the files and you would have a normal offline save.
The game goes into "Online mode" rather than having it identify a save file as online save based on properties in the save file. Once you click on the "Play online" button in the main menu, the game switches to this online mode.
I took prevention against data corruption last version. When the GameJolt server returns any suspicious return values for saving online, it creates backup files that we can apply to your online save that will then be recovered to the state right before saving the game. If that ever occurs to you, just upload the backup file to the dedicated forum in the Support forum. These files also get created when the game crashes.
The save gets downloaded into RAM anyways, but I will not save the game on the harddrive while the game is in online mode.
So now to the requested feature:
I might enable the download of the GameJolt save sometime in the future, and just save the downloaded data as another offline save. The only problem I see right now might be the sprite that can't be retrieved in offline mode. And since you cannot get any Emblem points in offline mode, you would be stuck with your current trainer level sprite, for example the Waiter sprite.
But other than that, there's no real challenge in converting the online save to an offline save.