This is an old question, but it's gotten bumped, so I am sharing some old research that I was a part of about twenty-five years ago. There are not (to my knowledge) any archives of the bulletin board where this was discussed, but I remember the rough conclusions that we came to. We were coming to the question from the point of view of Dungeons & Dragons players, and we came to a D&D-related conclusion; however, we were not looking for evidence that had to come specifically from the game.
The word phylactery was based on a previous Greek word meaning, roughly, amulet, indicating a magical protective charm of a size to be carried on one's person. Phylactery was used both in this generalized meaning and in the specific meaning of tefillah, for essentially the entire history of the word. However, there were probably no instances of the soul jar meaning until 1979.
In the AD&D Monster Manual (1977), the lich was described as needing phylactery to maintain its state as a free-willed, thinking undead monster. At that point, the mention of the phylactery was just a bit flavor text, like that found in many of the Monster Manual entries. It is not clear which meaning of phylactery E. Gary Gygax had in mind, although he was extremely erudite and referenced all sorts of miscellaneous trivia in the AD&D game rules, so I suspect that he probably knew of the Jewish meaning. The accompanying artwork by David A. Trampier showed the monster wearing a crown, with a protruding block on the front that could be either a jewel or a tefillah.
While Gygax and Trampier may have known the religious meaning of phylactery, it appears that Len Lakofka may not have. In his article "Blueprint for Lich" (Dragon Magazine #26, page 36; later reprinted in one of the Best of Dragon anthologies), the process he describes (via which a wizard may become a lich) focuses on a soul object that the mage's life energy must be stored in as part of the process. Lakofka never used the word "phylactery" in the article, but it certainly appears that the Monster Manual phylactery and Lakofka's soul jar are meant to be one and the same. The connection was made explicit in the ENDLESS QUEST (like Choose Your Own Adventure) book Lair of the Lich in 1985.