How do we reconcile between the fact that sins can invalidate good deeds and the Hadith in Tirdmithi (2639)? Firstly, has it been classed as authentic by classical scholars and secondly, if a man had 99 scrolls of sins how could he have such a weighty good deed left (saying la ilaha illallah)?
If you say that was his faith, then how will some Muslims have no good deeds on the Day of Resurrection as per the hadeeth in Saheeh Muslim of Abu Sa'id Al-Khudri in which Allah will take a handful of believers who did no good from the Fire? How did they end up with no good deeds if doing good deeds is a requirement of iman and being a Muslim? In fact, it says they NEVER did any good, how can you be a Muslim but never have done any good?
Also, how do we reconcile that hadeeth in Saheeh Muslim and the hadeeth about the intercession of Muhammad (peace be upon him) for those with even a tiny bit of iman, I thought in that hadith his intercession takes out every Muslim, but it doesn't if Allah still intercedes. Also, does Allah only taking a handful mean some Muslims will not be taken out by any intercession and will only be taken out once they have paid for their deeds?

All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.

Our answer to your question can be summarized as follows:

First: The Hadeeth you referred to as cited in Sunan At-Tirmithi, if you mean the Hadeeth about the card and the man who will have ninety-nine scrolls of sins spread out for him, then this Hadeeth was narrated by Al-Haakim in Al-Mustadrak, and he said that it meets the conditions of authenticity stipulated by Muslim, and Ath-Thahabi agreed with him in this regard. It was also narrated by Ibn Maajah, Ahmad, Ibn Hibbaan, and At-Tirmithi, who classified it as Hasan (sound), as well as a number of scholars who classified it as authentic. Therefore, it is authentically attributable to the Prophet .

Second: the Sharee‘ah texts indicate that some sins of a lesser degree of gravity than Kufr (disbelief) are reasons for rending one’s deeds worthless. However, this does not contradict the Hadeeth about the card for two reasons. First, because the fact that a sin may cause good deeds to become worthless does not necessarily mean that those deeds would actually become worthless; Allah, The Exalted, may forgive the sinner and not render his deeds worthless because of that sin. Second, not all sins render good deeds worthless, and even the sins that do so would not render all one’s good deeds worthless. Muslim jurists commented on the Hadeeth that reads: “He who misses the ‘Asr prayer (deliberately), his deeds will be rendered worthless," saying: "It means that missing the ‘Asr prayer renders one’s deeds on that day worthless." Others said: "It means that the deed that would become worthless is the very prayer he missed, in the sense that he loses its reward." This opinion was mentioned by Ibn ‘Abd Al-Barr. This means that the sin does not render all one’s deeds worthless. Rather, what renders all one’s good deeds worthless is to die while adhering to disbelief as Allah, The Exalted, Says (what means): {And whoever of you reverts from his religion [to disbelief] and dies while he is a disbeliever – for those, their deeds have become worthless in this world and the Hereafter, and those are the companions of Hellfire, they will abide therein eternally.} [Quran 2:217] Scholars said that good deeds become worthless in two senses: first, deeds may become permanently worthless, and this happens in the case of disbelief, which renders one’s faith and all good deeds completely worthless. Second, deeds may become temporarily worthless, meaning that their rewards are suspended. This refers to the situation where sins cause their doer to be denied the rewards of his good deeds when the sins outweigh the good deeds. The situation continues as such until he is granted deliverance, and, at that point, he receives the rewards of his good deeds.

Third: The Hadeeth states that some people will come out of Hellfire although they had never done any good deed. This does not contradict the obligation of good-doing because scholars interpreted the Hadeeth to have either of the two following meanings:

The first is that they did not perform any physical good deeds (actions of the body), and this would refer to people who die before being able to perform any good deed. The Fatwa of the Permanent Committee reads: “As for the Hadeeth that says that some people will be admitted to Paradise without having done any good deeds, this is not a general rule that applies to all people who fail to do good deeds despite their ability to do them. Rather, it is particular to people who fail to do good deeds for an excuse preventing them from it.” [End of quote] Shaykh Ibn ‘Uthaymeen said: “It refers to people who die before having had the ability to do good deeds; they believed (in Allah) and then died before having been able to do any good deed. In this case, they fit the description mentioned in the Hadeeth, i.e. they never did any good deed.” [End of quote]

Accordingly, they would enter Hellfire not because they failed to do good deeds due to their inability but due to the sins they committed or the good deeds they were able to do but did not.

The second meaning is the scarcity of their good deeds. Ibn ‘Abd Al-Barr said: “This is common in the Arabic language; a term that refers to a ‘whole’ would be used to denote ‘some’ of that whole. For example, Arabs would say, ‘He never did such-and-such’, meaning that he did very little of it.” [End of quote] This is evidenced by the Hadeeth which states: “There was a man who never performed any good deed, but he used to lend money to people, and he would say to his messenger (whom he sent to collect from the debtor): ‘Take what they can pay easily, and show leniency to the insolvent person who finds difficult to repay; forgive them (renounce all or some of their debts), perhaps Allah, The Exalted, would forgive us.’ When he died, Allah, The Exalted, Said to him: ‘Did you ever do any good deed?’ He said: ‘No, but I had a slave and I used to lend people. When I sent him to collect the debts, I would say to him: ‘Take what they can pay easily and show leniency to the insolvent person who finds difficult to repay; forgive them (renounce all or some of their debts), and perhaps Allah would forgive us.’’ Allah, The Exalted, Said: ‘I have indeed forgiven you.’” The Hadeeth describes the man as one who never did any good deed although he used to lend people money and drop their debts (or part of it). Thus, it becomes clear that the intended meaning is that he only performed a few good deeds.

Fourth: The Hadeeth about the intercession, which states that Allah, The Almighty, would take a handful from Hellfire, bringing out of it people who never did any good, indicates that the intercession of people for one another on the Day of Judgment will not accommodate all those whom Allah, The Exalted, would take out of Hellfire.

Allah Knows best.