Yes i did do that but now that i got over the feeling of total clusterfuck (that i apparently created) i just hate being railroaded by the writer's decisions that are absolutely opposite of mine. Now I just feel like it's an entirely different game with someone else's choices...I know Stan5851 has already responded about how saves for Renpy games work. Your problem from what you have told us is that you overwrote ep3 with ep 4. They are obviously separate files with there own exe's. Just like ep3 was to ep2 and ep2 to ep1. From your surprise at where some paths are at the start of ep4 I would guess that you never finished ep3. I would suggest you download ep3v16 that is shard here, finish all the content there and then move on to ep4. Ep4 start should make more sense this way.
But if not that is okay. Take away the wine and cheese and add whiskey, I'm as happy with life as Stan5851 .
Anyways, that's just me... Enjoy the game.