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Before proceeding, it is crucial to note that in the overall scheme of a question attention should be paid to detailing sources. In your question, unfortunately nothing like this has taken place. For example, in the question, there is no mention of which Shia scholar you spoke to and in which books, and which hadiths were referred to (which can no longer be found in the Six Authentic Books of the Sunnis). It would have been better if you could have mentioned some references for all of these aspects of your question so that it could be researched on our end and a more precise and exact answer could be given to you.
Irregardless, it can generally be said that some of the Shia scholars have made such claims and have expressed their reasons for believing in this idea. For example, it has been said that sections of the text of Sahih Bukhari, which openly shows opposition of the second Caliph to a command of the Holy Prophet (s), has very clearly been removed from the books now in print. For reference please refer to the Research Institute of Waliye Asr (AF) who has posted images of different manuscripts of Sahih Bukhari in which distortion has taken place.
In modern times, technologies such as microfilm, digital data storage, and also libraries which contain massive quantities of books have made the possibility of alteration much less. Even in the case of alteration, these technologies have made the chance of discovery rise exponentially, thus it can't quite be claimed that these sources have undergone alteration in this age. Nevertheless, the same doesn’t apply to past times and there are chances of such taking place. Two main ways exist to prove that a text was indeed altered in the past. The first is if we can actually get hold of several editions of a book and then show that parts of the book were no longer there in later editions. The second way is to find a reference to a source in another authentic book and not being able to find the referred hadith in that source, which indicates that during the time of the compilation of that authentic book, the hadith existed, but can't be found today.
Some people believe that such alterations did take place in Sahih Bukhari. For example, things have been narrated from this book in its commentaries, that cannot be found anywhere in the book itself.
In this field there is some evidence that points to the validity of this theory. In the book ‘Fathul Bari’, which is a commentary on Sahih Bukhari, it has been narrated from Qurtubi who is the writer of ‘Mukhtasar Al Bukhari’, that he said that in the book of Al Ashribah (drinks) of Sahih Bukhari I personally saw that it was written: "قال أبو عبد الله البخاری رأیت هذا القدح بالبصرة وشربت منه وکان اشترى من میراث النضر بن أنس بثمانمائة ألف", which means that Bukhari said: “I saw this cup (the cup which the Holy Prophet (s) would drink water out of) in Basra and I drank water out of it. This cup had been bought from the inheritance of Nadhr Bin Anas with 800,000 Dirhams. This line could not be found at all in Sahih Bukhari and the writers of these commentaries were not from amongst the Shias so that it could be said that they had, through their own desires, falsely added things to Sahih Bukhari.
Some of the scholars and researchers amongst the Ahlul Sunnah have said that it’s not correct to call such things as alterations because nothing has been decreased from the actual tradition and it is only the personal opinion of individuals or the opinion of Bukhari (the writer of the book) which has been removed. Of course it has to be known that this attempt at explaining away this issue is not suitable. This type of change, even if it’s not considered a clear cut alteration, is at the very least, a type of alteration and may distort the meaning of the narrated tradition.
Now we will move on to the question of what reasons exist behind such alterations. The answer to this is that we Shias believe that our school of thought can be proven even through the books of the Ahlul Sunnah. It’s natural that the opposing side, in the face of such a claim which reaches into even the most authentic of Sunni books, is forced to either declare defeat or resort to removing and reediting parts of their books of tradition. The seeker of truth will pick the first path, while an obstinate individual will pick the second path. This analogy naturally does not apply to the oppressed masses that are living in a hostile environment and are not able to reach the truth.