Recircumcised?

2 At that time the Lord said to Joshua, “Make flint knives for yourself, and circumcise the sons of Israel again the second time.” 3 So Joshua made flint knives for himself, and circumcised the sons of Israel at the hill of the foreskins.(Joshua 5:2-3)

God commanded Joshua to see that this was done to all males under 40. These were sons of the generation who died in the wilderness, survivors (cf. vv. 6, 7) from the new generation God spared in Num. 13, 14. This surgical sign of a faith commitment to the Abrahamic Covenant (see Gen. 17:9–14) had been ignored during the wilderness trek. Now God wanted it reinstated, so the Israelites would start out right in the Land they were possessing.

This was not a re-circumcision of individuals (which would be impossible), but the second occasion of doing this as a nation. This implies that as a nation it had been done before leaving Egypt (Josh. 5:4), but those born in the wilderness were uncircumcised ( Josh. 5:5). This also implies that there were many ways that the law was not kept during the wilderness wanderings.

This circumcision was necessary because the generation that came out of Egypt had fallen under God’s judgment. In His grace God was raising up a new generation for Himself (v. 7). Physical circumcision had its spiritual counterpart in circumcised hearts (Deut. 10:16; 30:6)

When God reaffirmed his covenant with Abraham, promising him the land of Canaan, he warned him that anyone who was not circumcised would be violating the covenant (Gen 17:7–14). Consequently, Israel could not claim the covenant land until the sign of the covenant had been restored. Here is another parallel between Moses and Joshua: When called to lead the covenant people out of Egypt, Moses had to restore the the covenant of circumcision in his own family (Exod 4:24–26). In the instructions God gave Moses for the Passover meal, no uncircumcised males were allowed to participate (cf. Exod 12:48–49). Circumcision may have been a puberty rite in some nations, but for Israel it marked one’s entrance into the covenant community. In Hebrew this verse is redundant; it says, “Circumcise the Israelites again, a second time.” There is no record that Joshua conducted any mass circumcision prior to this, nor was anyone to be circumcised over again. Joshua was reinstituting circumcision after it had been neglected during the forty years in the desert.

It is interesting that not even Joshua had circumcised his children while in the desert:
7 Then Joshua circumcised their sons whom He raised up in their place; for they were uncircumcised, because they had not been circumcised on the way. (Joshua 5:7)

This was a reproach to him in God's eyes:
9 Then the Lord said to Joshua, “This day I have rolled away the reproach of Egypt from you.” Therefore the name of the place is called Gilgal to this day. (Joshua 5:9)

That reproach was removed by the act of circumcision that renewed the Abrahamic Covenant and affirmed God's commitment and faithfulness to His people and Joshua's place in His plan.

This is borne out by the reaffirmation made at the end of the chapter by the appearance of the Angel of the Lord:

13 And it came to pass, when Joshua was by Jericho, that he lifted his eyes and looked, and behold, a Man stood opposite him with His sword drawn in His hand. And Joshua went to Him and said to Him, “ Are You for us or for our adversaries?” (Joshua 5:13)

This man proved to be one of the Persons of the Trinity who was personally leading Israel from Egypt. From all outward appearances Joshua thought He was a man. He stood like a man, looked like a man, held a sword like a man, spoke with an audible voice like a man, and Joshua approached Him like a man.

Five proofs that He was God, not a man: 

1. He claimed to be Captain of the host of the Lord. Joshua knew God was the Captain of Israel. He had promised to go before them and lead them into Canaan, and had done so for forty years ( Ex. 3:8 , 12 , 17-22 ; 6:1-8 ; 10:2-6 ; 23:20-33 ; 33:1-3 ; Josh. 1:2-9 ; 3:7-8 ; Acts 7:31-37 ).
2. Joshua worshipped Him, and such reverence belongs only to God. If He had been only a messenger of God, He would not have permitted worship (cp. Rev. 19:9-10 ; 22:8-10 ).
3. Joshua called Him "Lord" (Hebrew: 'Adon (H136 h136 ) sovereign; lord; master; owner).
4. Joshua recognized himself as His servant.
5. The same thing was said to Joshua that was said to Moses. Only God could make such a demand (cp. Josh. 5:15 with Ex. 3:1-8 ).