A creature with a Bardic Inspiration die can roll it to add the result to an ability check, saving throw, or attack roll, while the Divination wizard's Portent feature overrides the roll before the roll is made.

Because the roll has never been made, does this mean that a roll replaced by Portent cannot be improved by the Bardic Inspiration die?

Yes, in fact you can.

According to official 5e rules designer Jeremy Crawford, in this tweet:

@IgnatiusJRiell The portent die is intended to replace a d20 roll only, not any modifiers applied to it.

Portent only replaces the die roll, not the entire check; bonuses can then be added, including Bardic Inspiration.

Yes, you can add Bardic Inspiration to a roll replaced by Portent

The Divination wizard's Portent feature says:

You can replace any attack roll, saving throw, or ability check made by you or a creature that you can see with one of these foretelling rolls. You must choose to do so before the roll, and you can replace a roll in this way only once per turn. (PHB, p. 116)

The rules state that you can replace a d20 roll from any of three types (attack, saving throw, or ability check) with a roll made with portent. The reason this gets confusing is because it is not clear at first if Portent is replacing the roll for these things or the entire attack, ability check, or saving throw.

Ability checks, saving throws, and attack rolls consist of a d20 roll + modifiers, not just a roll:

To make an [ability check/saving throw/attack roll], roll a d20 and add the relevant ability modifier.

(The line is exactly the same for all three so I have combined them for convenience.)

But later in the ability description it makes it clear that Portent is only meant to replace the roll (the d20 roll) in each of these not the entire roll + modifier:

you can replace a roll in this way only once per turn

This means that the roll, even after being replaced by Portent, is still considered to be part of an ability check, attack roll, or saving throw and is thus still qualified to have modifiers added. This includes Bardic Inspiration which says:

Once within the next 10 minutes, the creature can roll the die and add the number rolled to one ability check, attack roll, or saving throw it makes.

The fact that, because of Portent, the roll was "pre-decided" does not have any bearing on the fact that the roll is still modified in the normal way as if the d20 had been rolled.

Rules as Intended agree

Jeremy Crawford has clarified and made it clear that the above reading of the RAW is correct and as intended in this tweet:

The portent die is intended to replace a d20 roll only, not any modifiers applied to it.

Thus, Bardic Inspiration still can apply to the roll.

Bardic Inspiration is used to boost the activity a PC is carrying out now:

Once within the next 10 minutes, the creature can roll the die and add the number rolled to one ability check, attack roll, or saving throw it makes.

The Divination wizard's Portent feature (PHB, p. 116) is used to replace a roll made, with the value they originally rolled:

You can replace any attack roll, saving throw, or ability check made by you or a creature that you can see with one of these foretelling rolls. You must choose to do so before the roll, and you can replace a roll in this way only once per turn.

Since Portent is not a saving throw, attack roll, or ability check, and there is no roll when Portent is applied, they cannot be affected by Bardic Inspiration.

However, this can be allowed by the DM if they so choose.