Here the 1841 British edition accidentally switched the word order, moving once before the subject pronoun it. But the subsequent LDS edition (in 1849) restored the original word order. Either order, “when it once hath had place in you” versus “when once it hath had place in you”, is possible. The critical text will maintain the original order (which is extant in 𝓞), with once after it.
Summary: Maintain in Alma 39:6 the placement of once after the subject pronoun it (“when it once hath had place in you”).