More likely than not, she’s just fucking with him because she has known for quite some time that the first officer was “hiding” the stuff in her ship, and it’s just a coincidence that she threatened him with it.
Yea, I figured as much, and I don’t buy my suggestion in the parent post, but it’s still odd they leave it hanging especially given the huge implication that isn’t so easily dismissed.
It’s also imminently possible you’re right, but the Relativity or someone else from the 29th century has been busy undoing the damage such widespread awareness of the future events would cause.
Chakotay’s vision of the future was also not the future that ultimately ended up existing. In such a world, the Relativity probably left him alone, as his foreknowledge wasn’t particularly useful, and they could simply look at some Starfleet records and see if he ever shared what he knew in a way that would affect the future. On seeing that he didn’t, they opt to not intervene.
Meanwhile, Janeway has shown time and time again to do whatever the fuck she wants with the timeline, and Captain Braxton probably relished pulling her in, zapping her memory of those events, and dumping her back into her own time.