Many objects deleted upon updating to version 1.4.5.64

Upon launching KSP after installing this update using CKAN, most of the objects of one of my bases disappeared. The lost objects include a stock KSC runway and various objects from the Kerbinside assets collection.

At least some, and probably all, of the affected instances appear to still exist in instance list files. These instances do not show up in the list of the in-game editor. Vessels previously landed on top of them fall through the now empty space to the ground.

An example of a file specifying a disappeared instance is below.

// Generated by Kerbal Konstructs

STATIC
{
    pointername = KSC_Runway_level_2
    Instances
    {
        UUID = 7d2b35a5-cf3f-4bf2-b3c2-8d6f42362a02
        CelestialBody = Kerbin
        RelativePosition = 1023.55664,8.65130615,13.7614746
        Orientation = 0.0977289453,88.8319626,-0.000687071879
        isScanable = False
        ModelScale = 1
        //old
            //VisibilityRange = 25000
        //new
            VisibilityRange = 100000
        Group = COLE
        GrasColor = 0.0809368193,0.112854056,0.0504357405,-0.0624183156
        LaunchSite
        {
            FacilityType = KKLaunchSite
            OpenCost = 0
            CloseValue = 0
            FacilityName = 
            LaunchPadTransform = End09/SpawnPoint
            LaunchSiteName = COLE
            LaunchSiteAuthor = Squad
            LaunchSiteType = Any
            LaunchSiteLength = 0
            LaunchSiteWidth = 0
            LaunchSiteHeight = 0
            MaxCraftMass = 0
            MaxCraftParts = 0
            InitialCameraRotation = 90
            LaunchSiteIsHidden = False
            ILSIsActive = False
            OpenCloseState = Closed
            Category = Runway
        }
    }
}

GER-Space / Kerbal-Konstructs

Many objects deleted upon updating to version 1.4.5.64 #137