Color Layering issue

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I am currently printing parts in two colors. The part I'm printing right now, came out great initially, but I noticed a modeling issue towards the outside of the object and had to correct it. Other than that, it came out perfect. Now, an unrelated part towards the inside of the object that is supposed to print green only, is layering black and green (alternating between the layers which color it prints). I checked it in the model, and the parts aren't intersecting and haven't moved since the first print where this part of the object came out perfect. In Cura, it does show the center piece alternating between colors, but why? and how do I fix this? 

 

Brief recap-

Two color print came out well, save for a modeling issue at the outside

Fixed modeling issue on outside

Part I didn't touch is now layering the colors.

Fix?

 

I have posted in many FB groups to find the answer, but nothing yet. Please help. I'm not sure how to get this small piece to print right again. Now I have two parts that printed perfect, with a different exception for each. Now if I can get the best of both prints, I'll have the exact part I need.