Potential Major Issue With Saved Files Since Update

I've been using Illustrator to do apparel designs and I often need to reference different files to either grab things from them or save a copy so that I can recolor them. Since the most recent update many of my saved files have very strange issues. For instance, there are certain parts of the design I can click on and everything is just fine; the swatches will display the correct color and if I try changing the color it works like normal. However, there are other areas where on screen the object shows as one color (blue, for instance), but the swatches show the object as black and as the stroke, not the fill, which only adds to the weirdness. If I attempt to change the color, the swatches themselves will switch to whatever color I choose, but the on screen object remains the same color. I've checked to make sure nothing was locked or that I wasn't accidentally clicking a different layer. I'm perplexed by this and hoping someone has an answer beyond, "Tough luck, your file is ruined."