Ok, I just had this happen to me for the first time.
I finished a chapter, saved it, and moved to the next chapter. As I was starting the new chapter, I scrolled up in Logos to look at the end of the chapter I had just finished, and when I did so, it dragged Paratext to the end of the previous chapter as well. A message popped up saying that the chapter had changed from 48 verses to 1, and asked me if I really wanted the change. So in this case, it definitely occurred when another program dragged Paratext along.
Another item which might be important to note, there were unsaved changes in the new chapter I was working on, and when I said that I wanted to save those changes, it saved them, but also put the material from that chapter into the previous chapter.
I would like to see Paratext have an option to only send (and not receive) references, as usually I don’t want the passage I am working on in Paratext to change on me. However, I don’t know how easy it would be to implement something like that.