As you say, “ly” is an early form of the Romance article; you can compare the Old French article for nom. sing. masc. "li". Aquinas uses it in his commentary on the Gospel of John 1,1 explicitly as the equivalent of the Greek article in its specifying sense:
Ut ergo Evangelista hanc supereminentiam divini verbi significaret, ipsum verbum absque ulla additione nobis absolute proposuit; et quia Graeci, quando volunt significare aliquid segregatum et elevatum ab omnibus aliis, consueverunt apponere articulum nomini, per quod illud significatur sicut Platonici volentes significare substantias separatas, puta bonum separatum, vel hominem separatum, vocabant illud ly per se bonum, vel ly per se hominem ideo Evangelista volens significare segregationem et elevationem istius verbi super omnia, apposuit articulum ad hoc nomen logos, ut si dicatur in Latino, ly verbum.
In other words: “ly verbum” means “ὁ λόγος”.