Magwitch the criminal gets Pip to steal several items from his house in order to help him escape. One of those items was Joe's file, which is like a saw, for metal. Magwitch, and his criminal friend, must have used the file to saw off their handcuffs; the cuffs are later discovered by the soldiers, but the file is not found.
Later on, in chapter 10, Pip goes to the local tavern where a stranger is sitting; lo and behold, he has the file. He is using the file to stir his drink, and he stares at Pip, making him very uncomfortable. Pip realizes that this must be the second criminal, Magwitch's fellow escapee. The man later gives Pip money, most likely in thanks for helping him to escape. So, Joe's file, used to help two criminals escape, turns up 7 chapters later in the hands of a mysterious man who gives Pip money. It is an interesting development. I hope that helped; good luck!
The object in Chapter 3 would be the File the convict uses to cut the iron off of his leg. Not only does the one convict Pip runs into need the file, but the other convict you run into earlier in the chapter needs it too, also of which to cut the iron off of his leg.