In my own personal continuity, the "war" timeline as seen in YE is the "real" one. As for Guinan's perceptions in the war timeline, they can be explained by her being deep, deep, deep cover Section 31 working for or even with people to manipulate history, whether they are Federation time police, or some other agency or party.
One possible theory is that the Federation Department of Temporal investigations (or it's 2344 counterpart) made note of the temporal rift and later investigation by Starfleet Intelligence found that the Enterprise-C may have fell into it. They eventually calculated it's target point in space and time and it was kept classified.
Years later, with the Federation months from surrendering to the Klingon Empire, Starfleet being beaten, Section 31 arranged to have the Enterprise-D near the location of the rift. They used their operative Guinan who'd been friends with Picard for years and had earned his trust, to come up with some story about the timeline feeling wrong in order to convince Picard to send the E-C back and thus we have the TNG timeline we all know and love.
It could happen lol.