The Gemora has a dispute between Rabbi Meir and Rabbi Yehudah whether the Torah scroll that was written by Moshe was actually in the Ark with the Tablets, or whether it was in the on the side of the Ark.
The Gemora (14b) refers to this Torah scroll as the scroll of the Temple Courtyard. Why would the scroll that is kept inside the Holy of Holies be called the scroll of the Temple Courtyard?
Rashi is apparently bothered by this question and says that the scroll that Moshe Rabbeinu wrote was used by the king during hakhel, and by the Kohen Gadol on Yom Kippur. Apparently, Rashi held that it was permitted to go into the Holy of Holies to take out the Torah in order to read it.
Tosfos (14a) asks why the Gemora finds it necessary to leave some space in the Ark so that the Torah can be put in and removed easily; it was never removed anyway, since it is forbidden to enter the Holy of Holies except on Yom Kippur, and we don’t find any mention in the Mishnayos that they would use this Torah scroll on Yom Kippur!?
Tosfos clearly assumes not like Rashi and holds that this scroll wasn’t used, and is therefore troubled by why they had to leave space to get it in and out easily.
Tosfos answers that although it was never used, they would sometimes remove it in order to repair it (and one may enter the Holy of Holies in order to fix it, so too, one may enter to fix the Torah scroll). Also, between the destruction of the Tabernacle in Shiloh and the second Temple, they would use the Torah.
The Reshash suggests that even Rashi agrees with Tosfos that one may not enter the Holy of Holies to remove the Torah, but during the second Temple, when there wasn’t any Ark, it was used (and that is why it is called the scroll of the Temple Courtyard – for perhaps during that time, it was actually kept in the Courtyard).