1. All Jewish communities had many converts, which usually required forgery of yichus records to conceal they were converts since conversion to Judaism was usually a capital offense (considered to be heresy which was related to treason). How do you think Ashkenazim got to be so light skinned with many blonds among us?
2. There has always been substantial migration between Yemen and the Horn of Africa. And Yemen has had a well documents Jewish community. It should also be noted that the Ethiopian goyim have many customs that appear to be of Jewish origin, and that Jews in adjacent regions (Egypt and Yemen) were aware there were Jews in Ethiopia. The Ethiopean Christians knew there were Jews in their county and persecuted them.
3. If a Jewish community doesn’t emphasize learning Torah, their observances are likely to become corrupted over time. A Jewish community of Baal ha-Batim that doesn’t support a community of “batlanim” will mess up a lot. That would explain the halachic errors of Ethiopean Jews (and many others isolated Jewish communities – you really can’t be properly frum without a strong commitment to learning Torah).