She got pregnant before she started to make up missed fasts, and she cannot fast
Question

My wife owed some days that she did not fast last Ramadaan because of her menses, but before she formed the intention to fast those days before the next Ramadaan, she got pregnant, and the doctor told her that she should not fast at all during her pregnancy and possibly during the breastfeeding period too, because of her general weakness and fearing for the foetus. Hence she will not be able to fast these days. What should she do about these days? What should she do if she cannot make up the days of the next Ramadaan before the following Ramadaan comes?.
Praise be to Allah.Allaah has given the one who missed some fasts because of a legitimate excuse until the following Ramadaan to make up those fasts, but the Muslim should not use this as an excuse to delay making them up, because he may be faced with some need or changes that make it too hard for him to make them up or prevent him from doing so, especially women who may become pregnant, or be faced with menstruation and nifaas (postpartum bleeding). 
Whoever delays making up the fast with no legitimate excuse until there is very little time left, then Sha’ban ends and he has not made up the fasts he owes, is sinning, but if he has an excuse then there is no sin on him. In either case he has to make up those fasts after the second Ramadaan. Some scholars stated that he also has to feed one poor person for each day. If he is able to do that then that is on the safe side, otherwise making up the missed fasts is sufficient. 
See also questions no.  26865 and 21710. 
Shaykh Muhammad Saalih al-‘Uthaymeen (may Allaah have mercy on him) was asked: What is the ruling on one who delays making up missed fasts until the next Ramadaan comes? 
He replied: 
Delaying making up missed Ramadaan fasts until the next Ramadaan comes is not permissible according to the most well known scholarly opinion, because ‘Aa’ishah (may Allaah be pleased with her) said: “I would owe Ramadaan fasts and I would not be able to make them up except in Sha’baan.” This indicates that there is no concession after the second Ramadaan. If a person does that with no excuse, then he is sinning, and he must hasten to make up those fasts after the second Ramadaan. The scholars differed as to whether he must also feed the poor or not. The correct view is that he does not have to feed the poor as well, because Allaah says (interpretation of the meaning): 
“but if any of you is ill or on a journey, the same number (should be made up) from other days”
[al-Baqarah 2:184]
Thus Allaah did not enjoin anything on people in this situation apart from making up the missed fasts. 
Majmoo’ Fataawa al-Shaykh Ibn ‘Uthaymeen, 19, question no. 357. 
The Shaykh was also asked: 
A woman did not fast some days of Ramadaan last year, then she made them up at the end of Sha’baan. Then her period came and lasted until Ramadaan began this year, and she still had one day to make up. What should she do? 
He replied: 
She has to make up that day that she was not able to make up before Ramadaan began this year. When this Ramadaan ends, she has to make up what she missed from the Ramadaan of the previous year. 
Majmoo’ Fataawa al-Shaykh Ibn ‘Uthaymeen, 19, question no. 358. 
And he was asked: 
A woman did not fast during Ramadaan because of nifaas (postpartum bleeding), and she was not able to make up the fasts before the next Ramadaan came because of breastfeeding. What should she do? 
He replied: 
This woman should fast and make up the days that she missed, even if that comes after the second Ramadaan, because she was unable to make up the fasts between the first and second Ramadaans for legitimate reasons. But if it is not difficult for her to make up the fasts during the winter, even if she does it day after day, then she has to do that, even if she is breastfeeding. She should strive to do whatever she can to make up the missed Ramadaan fasts before the next Ramadaan comes. If she cannot manage to do that then there is no sin on her if she delays it until the next Ramadaan. 
Majmoo’ Fataawa al-Shaykh Ibn ‘Uthaymeen, 19/ question no. 360. 
To sum up:  These days remain a debt which your wife owes, and which she must make up whenever she can. 
And Allaah knows best.