‘At that time YHWH said to Joshua, “Make yourself knives of flint and circumcise again the children of Israel the second time.” '
This did not mean circumcising those who were already circumcised for a second time (see Joshua 5:7), but reintroducing circumcision as something to be carried out on those who had not been circumcised during the journey through the wilderness and what followed.
Circumcision was an ancient rite practised in both Egypt and Canaan, and Abraham, having arrived from the north, was told to adopt the practise as a sign of YHWH's covenant with him (Genesis 17). No one who was uncircumcised was to be allowed to eat the Passover (Exodus 12:44; Exodus 12:48). Thus Abraham circumcised the whole of his family tribe ‘the first time'. Then from Abraham to the Exodus the rite of circumcision on the eighth day after birth was carried out on every male child as a continuation of that ceremony. But the journey from Egypt had interrupted the rite, for no circumcision took place in the wilderness. Thus it had to commence as a group matter ‘a second time'. It had possibly not been seen as helpful for people to be circumcised while constantly travelling due to the days of soreness that followed, and we must presume that Moses considered that YHWH Himself had given them a dispensation from it for the period.
Joshua used flint knives for the performance of the rite, even though it was at a time when the use of metal was well known and metal knives were to hand. It is clear from this that the ceremony was seen as so sacred, and so ancient, that the original methods had to be followed. Moses' failure to circumcise his son had led to almost fatal illness until the situation was remedied (Exodus 4:24-26). A flint was also used there. The use of flint knives, freshly prepared from new flints, meant that the knives were naturally the equivalent of having been sterilised, which metal knives would not have been.
Circumcision was an ancient institution not limited to the family tribe of Abraham and was practised in Egypt in the Old Kingdom period. But there it was carried out during boyhood rather than at infancy. A sixth dynasty Egyptian tomb relief depicts a boy being circumcised, probably with a flint knife, and two prisoners of a Canaanite king depicted on a 12th century BC Megiddo ivory, were also circumcised. But it is clear that in Abraham's family tribe circumcision was not practised up to Genesis 17, and it was not generally practised in Mesopotamia from where Abraham came. Modern medicine has shown the value of circumcision in protecting the health of those who live in semi-desert conditions as it helps to prevent foreign bodies becoming trapped under the foreskin.