Lost History - Can We Repair It?

[Faster]

On a career mode setup in 0.90 I'm noticing past events, e.g., successfully orbiting Kerbin, reaching Mun, are being forgotten and new "be the first to X contracts" are being generated. At first I thought this was a contracts bug, but then I noticed that if I sent different Kerbals, then Final Frontier would award them "first to X" ribbons making me think the problem is deeper in KSP than its contracts code.

My question is: can I repair this, e.g., by editing persistence.sfs (now and as the symptom repeats throughout the play-through)?

Here's the snippet of persistence that seems relevant (note: the game currently (again) thinks no Kerbal has reached Mun's SOI):

SCENARIO
    {
        name = ProgressTracking
        scene = 7, 8, 5
        Progress
        {
            FirstLaunch
            {
                completed = 120716.973798846
            }
            FirstCrewToSurvive
            {
                completed = 121416.258603572
                crew
                {
                    crews = Jebediah Kerman
                }
            }
            AltitudeRecord
            {
                completed = 447870.213549721
                record = 70000
            }
            ReachedSpace
            {
                completed = 447870.213549721
                vessel
                {
                    name = Meatball 3
                    flag = Squad/Flags/retro
                }
                crew
                {
                    crews = Jebediah Kerman
                }
            }
            Spacewalk
            {
                completed = 1269197.37314923
                crew
                {
                    crews = Jebediah Kerman
                }
            }
            Kerbin
            {
                reached = 120677.913798839
                Orbit
                {
                    completed = 599472.988429759
                    vessel
                    {
                        name = Meatball 4
                        flag = Squad/Flags/retro
                    }
                    crew
                    {
                        crews = Jebediah Kerman
                    }
                }
                Escape
                {
                    completed = 3535224.98060267
                }
                Landing
                {
                    completed = 120677.953798839
                    vessel
                    {
                        name = Jebediah Kerman
                        flag = 
                    }
                    crew
                    {
                        crews = Jebediah Kerman
                    }
                }
                Splashdown
                {
                    completed = 121384.218603565
                }
                SurfaceEVA
                {
                    completed = 120677.913798839
                    crew
                    {
                        crews = Jebediah Kerman
                    }
                }
                FlagPlant
                {
                    completed = 1409464.37108338
                }
                ReturnFromOrbit
                {
                    completed = 600525.815656174
                    vessel
                    {
                        name = Meatball 4
                        flag = Squad/Flags/retro
                    }
                    crew
                    {
                        crews = Jebediah Kerman
                    }
                }
            }
            Mun
            {
                reached = 3535224.98060267
                Flyby
                {
                    completed = 3535224.98060267
                }
                Escape
                {
                    completed = 3537471.86158694
                }
            }
            Minmus
            {
                reached = 5111324.97396296
                Flyby
                {
                    completed = 5111324.97396296
                }
                Escape
                {
                    completed = 5126889.85694749
                }
            }
        }
    }

[update] Corrected prefix.

Edited March 24, 2015 by Faster