Off and on I have found that "Replace with Passage" was not working on my Mac in Yosemite 10.10.3 with various versions of Logos 6.3. I would get it working then for some unknown reason it would not work.
Here is what has worked after I had freshly downloaded 6.3.0056 (6.3 SR-1) this morning and "Replace with Passage" didn't work.
You have to meet the following prerequisites:
1. Once Logos is totally signed in, Open your Word processing app.
2. The first time you highlight a reference to be replaced, if you highlight even one space after; along with the reference it will fail to auto replace.
3. Once you have highlighted a reference without any extra spaces after it, and successfully replaced the reference with the passage, it Works
4. Subsequent highlights/replaces with an extra space highlighted will sometimes work, (This is what was throwing me off) - When they fail: make sure to highlight without highlighting extra space after the reference and the "Replace with Passage" function works.
Have a Blessed Day!