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The five "churches," or religious eras, of humankind
According to Emanuel Swedenborg (1688-1772), there have been five major "churches," or religious eras, in the spiritual history of humankind. In the traditional English translations of his original Latin terms, they are known as:
These "churches" are not denominations, but rather key religious dispensations that, in their time, form the closest link with God among the various nations, cultures, and religions of humankind.
Swedenborg's commentary on Amos 3:2
Amos 3:2 reads:
You only have I known
of all the families of the earth;
therefore I will punish you
for all your iniquities. (NRSV)
Swedenborg did not write a full commentary on the book of Amos. There are scattered explanations of some of the verses in that book. However, the only direct commentary by Swedenborg on Amos 3:2 is found in his unpublished manuscript, Draft on the Inner Meaning of Prophets and Psalms. As its title indicates, this manuscript provides a very brief and sketchy running spiritual sense commentary on all of the Prophets of the Old Testament, and on the Psalms.
The commentary on Amos 3:1-2 in Prophets and Psalms (#203) reads:
The church was instituted solely with the Israelitish nation, therefore falsities and evils must be examined there.
The meaning of Amos 3:2 based on Swedenborg's theology
As indicated in the above quote from Prophets and Psalms, from the perspective of Swedenborg's theology, Amos 3:2 is speaking poetically of the Israelite nation and religion as the key "church" or religious dispensation of its time. So when it says, "You only have I known of all the families of the earth," it is speaking of the Israelite people as the "church" or religious dispensation where God most fully revealed the divine truth to the world during that time period.
It is not saying that God had no awareness of the earlier or later religious dispensations, or of the other nations, cultures, and religions of the world. Rather, it is saying that God had a special relationship with the Israelite people among all the then-existing peoples of the earth.
This is in line with the meaning of the meaning and connotations of the Hebrew word יָדַע (yada`), "to know," which does not generally mean mere intellectual knowledge, but rather experiential knowledge, and often a direct relationship with the one known. For example, יָדַע is the word used in Genesis 4:1:
And Adam knew Eve his wife; and she conceived . . . (KJV, italics added)
Similarly, in Amos 3:2 the word "know" is speaking of a special, close relationship between God and the Israelite people.
This relationship, Swedenborg said, lasted from when the Israelite nation first formed at the time of the Exodus from Egypt and the giving of the Law from Mt. Sinai until the time of the coming of Christ, when Christianity superseded ancient Judaism as God's primary "church" or religious dispensation on earth.
Summary
From the perspective of Swedenborgian theology, then, the resolution of the issue posed in the question is that Amos 3:2 is speaking of "all the families of the earth" that existed during the era of the ancient Jewish or Israelite religious dispensation.
At that time, the Israelite nation was, among all the nations and religions of the earth, the one with which God had a special relationship, and through which God provided the revelation that forms the Hebrew Bible, or Old Testament.