I'd look at it directly if I had the time. Sadly, i don't. I used to have bad flowing rivers with no problems. I would look for things like PWP count, PWP where they dont belong, too many PWP like bridges. (I have 4, but i heard more than that will crash the game. Projects or other "stuff" in the town tree area, does the town have the default number of rocks, was the travel dock moved? Also, the save ID may be wrong, as in the save trying to be used isn't seen as most recent. These are all things off the top of my head. Can your friend recall the last things they edited? If they can try, reverting them may work.
This should be a teachable moment for your friend. ACNL is finicky and you should always make a clean backup, then test the edited save before deleting the backup. Good luck. Wish I could help more.