The gemorrah says that the people forgot which form of the letters were used for the end of a word and which form were used for beginning or middle of a word such as the mem, and that the neviim restored the tradition.
If the Aron was still around during the time of the neviim, or the sefer Torah that was discovered during King Yoshiahu, what was the problem?
Thank you, Y. Stein
This question is discussed at great length. One answer is that the forgetting occurred after Yoshiyahu hid the Aron with the Luchos (Rashba and Ritva, Megilah 2b). Rabeinu Chananel says that the majority of the people from the simple scribes forgot. But still, why couldn't the Sifrei Torah and Tefilin that were in use be checked?
The Ritva brings an explanation based on the Gemara in Sanhedrin 21a that, according to one opinion, Ashuris script was not in use until Ezra's time, even for Sifrei Torah; everything was written in Ktav Ivri (ancient Semitic script) (except for the Sefer Torah of Yoshiyahu; see what the Rashba and Tosfos write about Sefer Yoshiyahu). Only the original Luchos were in Ashuris, but due to the holiness of the script it was not used. Therefore, Ashuris was not well-known. In Ktav Ivri the end-letters do not differ from the letters when they come in the middle of a word. With the onset of the new usage of Ashuris, there was a need to re-establish what letters were used and when. (See Artscroll edition of Sanhedrin 22a, note 22 at length.)
All the best,
Reuven Weiner