Dhabu

I have also had this exact problem happen, twice now. Probe leaves Kerbal (and its moons) SOI en route to Eve, I do other stuff/missions for awhile (several sessions/days of RL time), and one time (out of many) I go to the Tracking Center and try to fly my probe, screen goes black/weird, I have to quit out, I come back, probe is gone. I'm using Kerbal Engineer for more VAB construction data, but otherwise KSP is unmodded. As with the original poster, it first happened to me in 0.23 or 0.24.