Problem is at the end of "Before and After" their is a mention that she is going to talk to Janeway about the Krenim. Janeway should have know about them when they first meet in "Year of Hell." One option though is when the timeship is destroyed it means the past, before Voyager encounters Krenim is also changed which means the entire series of "Voyager" might have been altered so the events of "Year of Hell" didn't happen like it did in "Before and After" but happened in a new altered way like it did in "Year of Hell." When we first see "Year of Hell" the entire timeline has already been altered but then it is altered yet again to what we see at the end of the episodes.That also explains why in Year of Hell they didn't know about the Krenim since the timeline had been altered
Jason