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Advocate
Advocate

I've encountered the problem you're talking about. To bypass this, I draw Lines over the generic annotation's masking region. Reload the generic annotation in your host family, then reload the family in your project, and try it out, the wires won't cross over the nested generic annotation. 

Basically it seems that in the nested generic annotation, region boundaries wont cut wires, but lines will, so I overlapped my region boundaries with lines.