Ibn Al-Arabi, who stated that 9:5 abrogated 124 verses, also said that it was itself abrogated by 9:29! Here are the two verses,
is claimed to have been abrogated by
To begin with, the people covered in 9:29 are different from the people covered in 9:5 and therefore there can be no abrogation. The people covered in 9:5 are the polytheist while the people covered in 9:29 are the Jews and the Christians which God has repeatedly distinguished from the polytheist.
But if we were to accept that the "people who were given the Book" are considered polytheist, then this is an example of one verse explaining the other, not abrogating it. 9:29 defines the limits of 9:5, i.e., it states that the fight must end when non-Muslim citizens agree to be pay defense tax. Not only is this fair since Muslim citizens pay the alms tax, but it is also reasonable since non-Muslims are not required to enlist in the army while Muslims are.
One interesting additional note that should not be overlooked about 9:29 is that it specifies a combination of criteria
for whom to fight. Taken together, Jews and Christians do not fit those criteria, IMHO, because they believe in God. In addition, Christians are particularly excluded from this verse, because they also believe in the Final Day.