I know it's been a while since you posted this but I'm wondering if you remember if this ended up working for you or if you ever figured out a solution. I'm running into the exact same problem right now and was thinking of replaying Mio's route yet again just to get rid of the Silver Medal but don't really want to go through all that if it won't solve the problem (I also should have already done "enter storehouse, leave immediately, get silver medal from well, return to storehouse" several times to get the silver medal when needed on my first play-through so not sure why it's showing that path as incomplete.)