tefillin with only 2 parshiyos?

The gemara in R"H tells us that R' Abahu made a takana to blow teruah, shevarim, and shevarim-teruah to cover all the bases of the different minhagim that had been in practice.  The Rishonim quote R' Hai Gaon as having asked how something as basic as shofar blowing that we do every year and is such an important mitzvah could have been forgotten.  How could there have been different minhagim -- everyone should have had the same mesorah of how to do the mitzvah.  

Achronim ask the same question about tefillin of Rashi/R"T.  People put on tefillin every day.  How could the correct way to do the mitzvah have been forgotten?

R' Yosef Messas offers an interesting answer: the parshiyos of shema and v'haya im shamo'a were not given until the 40th year in the midbar, as we only find them in sefer Devarim.  For the duration of the time in the midbr, the tefillin must have had only 2 parshiyos.  We also know that when Moshe died thousands of halachos were forgotten.  It could be that there was never a strong mesorah established as to how the last 2 parshiyos should be added.

This chiddush gadol, that the nature of the mitzvah changed from what was given at Sinai (which seems to fly in the face of the first Rashi in Behar), is entertained by the Kli Chemdah, who rejects it.  The Mishna writes that the 4 parshiyos of tefillin are m'akeiv each other -- it's all or nothing.  Asks the gemara (Men 34): peshita -- isn't this obvious?  If the mitzvah originally required only 2 parshiyos, why does the gemara think this is such a davar pashut?  Perhaps if one cannot fulfill the mitzvah as it ultimately was performed from year 40 in the midbar onward, one should still fulfill the mitzvah with 2 parshiyos as it was given at Sinai?  See R' Kasher in Torah Shleima here, and R' Ovadya's teshuvah in Yabia Omer I:3 footnote 10.