It is said: “At most, the ‘Miracles of the Qur’an’ and of Islam in general are probabilistic sets of evidence, since reasonable arguments can be made against them. Even if we take the evidence from biology (like evolution), archeology, or other fields to also be probabilistic evidence against Islam, why should the objective person choose the probabilistic set of Islamic evidences over and above the (stronger) probabilistic set of evidences from scientific observations, experiments, and their concomitant conclusions?” What is our response in this case?
The case for Islam is both properly basic (providing direct, non-inferential but rational warrant for belief) as well as inductive. How persuasive the case for Islam of course depends in part on the prior assumptions a person has, which may be justified or unjustified, rational or irrational. For example, I think (and the Qur’an would regard) the belief that the contingent universe lacks a necessary cause, that this fine-tuned universe was not designed, or that sentient life was created by wholly non-rational forces as objectively irrational beliefs—even if a very large number of extremely intelligent people whom I love and admire as my brothers in humanity hold these views because of their pre-existing (and I think unjustified) philosophical commitments to naturalism.
Anyways I think the inductive case for Islam should be extremely strong—certainly strong enough to warrant belief, but arguably strong enough to significantly defeat reasonable doubt—if all the relevant information is taken into account and properly understood. This includes the evidence from natural theology, the historical context of the Qur’an (especially the life of the Prophet ﷺ), the internal evidence for the Qur’an, and any other relevant lines of evidence. If the case for the Qur’an is strong, then in the case of apparent conflict with material evidence, then one should consider various possible ways the Qur’an as well as the material evidence could be interpreted to see if there are plausible solutions. Unfortunately people, both critics and believers of Islam, all too often look at the text and the material evidence too superficially, and quickly jump to the conclusion of a conflict without considering any sophisticated hermeneutic methods or interpreting the text or considering whether the material evidence yields a single conclusive interpretation (which is usually not the case in a field like archaeology).
Also, it may be possible that the properly basic warrant for believing in Islam is strong enough to defeat the semblance of contradiction with external evidence even if one does not have a good answer in that particular case.
 It could be argued that this is a question better posed to a formal Islamic theologian, but it was felt that it was good to take the views of a person who concentrates more on Qur’anic studies, since the Qur’an is held by our theologians to be part of the evidence that should necessarily lead the researcher to Islam.