Must a wife make up the last three days of Ramadan if she was pregnant and experienced istiḥāḍah bleeding on the twenty-seventh of the month, and then miscarried on the third day of Eid al-Fitr?

Yes, your wife must make up for the days she missed from Ramadan due to a valid excuse, as Allah Almighty says: "But whoever among you is ill or on a journey [during them, then the same] number of other days."