First: the file coming back is likely based on how the save was handled - if you had multiple versions of it, at any time, - to completely start fresh, I would go to the game folder, and delete the slots along with the saves - Slot file stores the header info for the game to associate with the new save files, if it says a save slot exists, it exists, if it doesn't, even if the file is there, the save doesn't exist to the game/engine.
As for lag spike - If you join the discord and dm me, I can help you out with that, when the time arises, as well as the other thing you mentioned, I can tell you what contributes to the lag, and how to mitigate some of it, and also what may be contributing to the other thing (more or less speculation)