I don't know what this should output, but 2 isn't it.

$ jq -nc '{"a":[1,2,3]} | .a[] |= empty'
{"a":[2]}

This is the result of the following property of |=:

If the right-hand side outputs no values (i.e., empty), then the left-hand side path will be deleted, as with del(path).

This property also introduces this annoying difference:

$ jq -nc '{"a":[1,2,3]} | .a = ( .a | empty )'

$ jq -nc '{"a":[1,2,3]} | .a |= empty'
{}