The first mistake the author makes is when he determines the start of the 3-9 years period. The period starts from the time when the verses were revealed at the time Byzantines had suffered a major defeat and
not when they started their counter-attack. According to Islamic sources, that period starts from 615 CE. In 9 years time (i.e. in 624 CE) although, the Byzantines had not achieved their
final victory, but they had, nevertheless, achieved a major victory against the Sassanids.
The author apparently commits the straw man fallacy. The verses don't talk about the Cross being lost is the defeat that is being talked about. They only talk about the Byzantine defeat in that area.
"The third verse states that the Romans were defeated in 'adna al-ard'. The word adna is homonymous, and so the verse can mean that the defeat occurred in either the nearest or the lowest land. Scholarly books translate adna to nearest, because the defeat of the Romans took place in the nearest area of the Roman land to the Arab region. Islamic scholars believe that adna could also mean lowest because recent studies show that the area of the Dead Sea basin, in addition to being the nearest Roman occupied land to the Arabian Peninsula, is also the lowest point of dry land on earth, reaching almost 418 meters below sea level.
Although history does not pinpoint the exact locations of all battles, the proximity of Damascus and Jerusalem to this area presents a strong support for this interpretation."
Source:
https://web.archive.org/web/20140504150013/http://www.onislam.net/english/health-and-science/faith-and-the-sciences/464520-the-fulfilled-prophecy-of-surat-ar-rum.html?the_Sciences=I don't know why the author inserts the defeat of the Byzantine empire by the Arabs in 634. The verses clearly are not talking about this event. I think he intended to include the facts about the Persian defeat by the Arabs instead of the Byzantine defeat. In which case again, the verses were not talking abut that event.
Then the author, apparently, commits a few red herrings. What was the relevance of Qur'an 9:5 or "Insha' Allah" here?
Another straw man, when was the destruction of the "Persian population" predicted? When did the verse talk about: Allah will "destroy" the Persians; they simply predict a reversal of fates, in favour of the Byzantine empire.
It apparently appears that the author is trying very hard to connect the verses about: "definite proofs" being shown to the people before their destruction, with this prediction; which I cannot see how ti could be acceptable or non-fallacious.
Additionally, reading the comments section on that website, it
does seem quite odd that the only thing a critic will have a problem with in that article is the translation of the Arabic word for "definite".