She fasted even though she was not sure about her ghusl following menses. Does she have to make up the fast?

Firstly: 

Waswasah may be treated with two easy remedies: 

1.

Remember Allah a great deal and obey Him. This is the way to attain peace of mind, stability and reassurance, and to ward off the Shaytaan and his whispers, as Allah says (interpretation of the meaning): 

“Those who believed (in the Oneness of Allaah — Islâmic Monotheism), and whose hearts find rest in the remembrance of Allaah verily, in the remembrance of Allaah do hearts find rest”

[al-Ra’d 13:38]

“Whoever works righteousness — whether male or female — while he (or she) is a true believer (of Islamic Monotheism) verily, to him We will give a good life (in this world with respect, contentment and lawful provision), and We shall pay them certainly a reward in proportion to the best of what they used to do (i.e. Paradise in the Hereafter).

98. So when you want to recite the Qur’aan, seek refuge with Allaah from Shaytaan (Satan), the outcast (the cursed one).

99. Verily, he has no power over those who believe and put their trust only in their Lord (Allaah)”

[al-Nahl 16:97-99]

“Say: “I seek refuge with (Allaah) the Lord of mankind,

2. “The King of mankind —  

3. “The Ilaah (God) of mankind,

4. “From the evil of the whisperer (devil who whispers evil in the hearts of men) who withdraws (from his whispering in one’s heart after one remembers Allaah).

5. “Who whispers in the breasts of mankind.

6. “Of jinn and men”

[al-Naas 114:1-6].

Ibn Katheer (may Allah have mercy on him) said in his Tafseer: Sa’eed ibn Jubayr narrated that Ibn ‘Abbaas said concerning the phrase “the whisperer (devil who whispers evil in the hearts of men) who withdraws”: The Shaytaan hovers around the hearts of the sons of Adam, and if a person forgets the remembrance of Allaah and becomes heedless, he whispers to him (waswasa), but if the person remembers Allah, he withdraws. This was also stated by Mujaahid and Qataadah. 

Al-Mu’tamir ibn Sulaymaan narrated that his father said: I was told that the shaytaan or the whisperer blows into the heart of the son of Adam at times of sorrow and times of joy, but if the person remembers Allah, he withdraws. End quote. 

2.

Turning away from the waswasah and distracting oneself from it, and not paying any attention to it or responding to it. This guarantees that it will go away and one will be cured of it. 

Although this remedy is difficult in the beginning, it becomes easier later on. All you have to do is strive and make the effort, and ask Allah for help. Allah says (interpretation of the meaning): “As for those who strive hard in Us (Our Cause), We will surely guide them to Our paths (i.e. Allaah’s religion — Islamic Monotheism). And verily, Allaah is with the Muhsinoon (good-doers)” [al-‘Ankaboot 29:69].  

Ibn Hajar al-Makki (may Allah have mercy on him) was asked about the disease of waswasah – is there any remedy for it? 

He replied: There is an efficacious remedy for it, which is ignoring it completely, even if one feels hesitant about doing so, because once a person stops paying attention to it, it cannot remain for long; rather it will go away after a short time, as those who were guided by Allah have experienced. But if a person pays attention to it and acts upon it, it will continue to increase until it drives him insane, and even worse than that, as we have seen in many of those who were tested by it and paid attention to it and to its devils. End quote from al-Fataawa al-Fiqhiyyah al-Kubra (1/149). 

Secondly: 

The end of menses is signalled by one of two signs: 

(i)Complete dryness such that if the women were to insert a piece of cotton and the like, it would come out clean with no trace of blood or yellow or brownish discharge on it.

(ii)Emission of the white discharge, a white liquid which is well known to women.

You should not hasten to do ghusl until you are certain that you have become pure. Al-Bukhaari (may Allah have mercy on him) said in his Saheeh: Chapter on the beginning and end of menses; women used to send cotton pads with traces of yellow on them to ‘Aa’ishah and she would say: Do not hasten until you see the white discharge, meaning thereby becoming pure from menses. 

It was also narrated by Maalik in al-Muwatta’, no. 130 

Thirdly: 

If you see complete dryness and do ghusl, then some brownish or yellowish discharge comes, that does not matter, because yellowish or brownish discharge after becoming pure is not menses, because of the hadeeth of Umm Salamah (may Allah be pleased with her) said: We did not regard the yellowish or brownish discharge after becoming pure from menses as anything important. Narrated by Abu Dawood (307); classed as saheeh by al-Albaani in Saheeh Abi Dawood. 

There is no shortcoming or sin on one who delays doing ghusl and praying until she is certain she has become pure. Rather this is what she should do, because it is haraam to pray when one is menstruating. 

Fourthly: 

If we assume that you did ghusl before you really had become pure, then you did not repeat your ghusl, your fasts on the first and second days were not valid, because you were menstruating. But on the following days your fast was valid, because in order to fast, it is not stipulated that one should have done ghusl following menses or janaabah. 

Based on that, if you saw complete dryness, then your ghusl was valid and your fast was valid. 

If you were too hasty and did ghusl and fasted before complete dryness occurred, then you have to make up the fast of the first and second day, but with regard to the rest of the month, your fast is valid and you do not have to do anything further 

Our advice to you is what we have stated above of the necessity of treating waswasah and ridding oneself of it, and not paying any attention to it.  

We ask Allah to guide and help you. 

And Allah knows best.