Ibn Al`Arabi, who was one of the scholars who said that 9:5 abrogated 124 verses, also said that the Jizya verse,
abrogated 9:5! See this post
for a discussion of this claim.
So if 9:5 was abrogated, does this make it unable to abrogate other verses since it has been invalidated?
Depends on the order of abrogation. Sorry, couldn't resist.
I suppose they meant it's all invalidated, 9:5 and all that it abrogated. That shrinks the Quran by about 143 verses.
Ibn Salaama said that the epilogue of 9:5 is what abrogated it, i.e., he thought that the opening of 9:5 gave a Carte Blanche to kill all polytheists even if they accept Islam
and then that license was curtailed and allowed letting them live if they accept Islam.
This cannot possibly be the opinion of a man of knowledge. That is why I must conclude that what they all talked about, when they talked about "naskh", was not abrogation, invalidation or annulment, but amendment.