Attribute management is (as the programmers say) "not trivial".
Many library parts assume that you have the default fills, materials, linetypes loaded so it creates problems when they are modified. There will also be (missing) fills assigned to materials if you haven't edited the material attributes to account for the changed fills.
This has been a problem for quite some time and there has been much complaining and many requests for improvements.
Certain fills should be kept at their default indexes (yes, it is a major pain not being able to edit them directly). The ones that come immediately to mind are #1 "Brick Common", #84 "Solid Fill", and #85 "Empty Fill". There may be others but if you put these three back in, it may fix things up a bit.