Some kind of level up character progression should be kept both in the save file and in the character builder itself. Items affecter might be what features, feats and skill buying is being acquired at which level and other such things as applying/removing new stuff like lycanthropy and such.
Items inclusion in this progression should be completely optional.
This might help with de-leveling a character (to check for different builds) and applying negative levels.
Currently the character builder gets often confused in such things as point spending for skills and tends to undo them in a messy way, often generating errors, especially if other conditions apply, such as Patfinder's favourite class skill bonus. Similarly acquiring feats is done in a messy way and if i level a character with multiple levels the builder does not understand the concept of feat progression and allows me to pick feats for very early levels in a way that ignores mechanics. For example if my character gains Pathfinders's blindvision via a class mechanic such as dragon disciple and i level up straight to level 15 to get all the features, i can select feats in an impossible way, such as getting blindvision feat tree and in the same character progression i can as well add some feat tree that would require extreme strength and could not have been selected with the initial stats, but only with the final ones.
Something that keeps track of this might help, but i am listing it as a completely new feature, since it would not be just a simple bug fix, but would possibly need extensive rework.
windows 10 creators' edition
I believe the feat selection which you describe acts properly. Pathfinder allows retraining feats, and during retrain you can select feats you didn't qualify for originally: http://paizo.com/paizo/faq/v5748nruor1gn#v5748eaic9r9h
If you add 15 levels at once it's correct to allow you to select features as if you were level 15 character. It's a feature I use very often when creating NPCs and wouldn't want it blocked. When I want to simulate my feat gain on level by level basis I add levels one by one.