After deciding to not use paths, but go for the dead grass walkways, I started laying down flowers where I didn't wan't the grass to die. After a bit, I had a great idea to just dig holes where I don't wan't to walk. After finishing, and saving, I closed the game. 5-6 hours laters I open up the game to come and find out their ALL GONE! So mad, but it's whatever. Don't make the same mistake as me, digging holes, do not stay after you save and close the game.
I have a hybrid garden closed in with bushes, with one empty spot to get in. I dig a hole at the entrance before saving, to stop my idiot villagers dumping flowers in there. The hole is usually there when I save, turn off, and start again.
It doesn't always do this. I have to re-dig it at some point during the day. ^_^