The Torah must be written by a scribe copying from a "checked" copy of a scroll. Originally, the copy checked was that written by Moses. Eventually, Ezra wrote an "official" copy that was used. The "Torah Codes" that have been found could not have been determined if any letters in the Torah or the "distance" between the letters had changed at all. For example, see Writing the Torah at Aish Hatorah.The Talmud discusses this. The navi in Melachim discusses how an original scroll was discovered by Hilkiah in the time of Yoshiyahu and recognized as the original scroll of Moshe.
Note that I do not claim anything about these "Torah Codes". That is just an example of something that could not have been done if any of the words in the Torah that they try to use had been changed. Since they rely on the count of letters between points, any change would have totally dirupted their calculations.