The replace/remove tool does not work as expected with lines of symmetry. The block on either side of the line of symmetry will be replaced, but they will both have the same rotation not mirrored rotations. Image demonstration:
Here we have a pair of circles which we want to smooth together
If we set xy&xz symmetry before using the replace tool to turn the corner cubes into tetras here is the result:
By contrast, if we place tetras next to the previously placed via replace tool, the tetras mirror as expected: