«وَإِنْ كُنْتُمْ فِي رَيْبٍ مِمَّا نَزَّلْنَا عَلَى عَبْدِنَا»
And if you are in doubt about what We have sent down to Our servant.
The issue is not to make in necessarily signal uncertainty in the divine speaker; instead, the hearers' actual or supposed condition is expressed through a conditional frame. Without considering the context, the past form kuntum does not mean merely “you doubted before but no longer doubt.”
The construction establishes a challenge for anyone in such doubt: if this is your position, bring a comparable counter-example. The communicative force is argumentative rather than hesitant.