^You're reading too much into it. Remember, in PoN/RtD, Geordi was back where he'd been at the end of PoD. His stint on the Challenger was referenced, but he was still back at commander's rank aboard the Enterprise. And there's exactly zero mention of Leah Brahms in PoN/RtD. So there isn't any major conflict between that duology and Dave's trilogy, except that one makes a passing reference to the events of IFM and the other doesn't.
It may not be explicitly stated, but Geordi's stint on the Challenger and promotion to Captain of Engineering, replacing Captain of Engineering Scotty infers that that part of the story took place too.
What we are left with is :
Some of it did happen.
Some of it might have happened.
Only a small part of it definitely didn't happen.
Chucking it out of continuity hardly seems worth the effort !