Hello Matt,
I assume you are trying to create interior elevations? When using the FLEX drawing set, ConDoc is using the current tag visibility, not forcing specific tags on/off. So ConDoc can’t make any assumptions about interior/exterior elements and locations. I would recommend using the section tool to create your interior elevations with the FLEX drawing set.
For more control, load the INTERIORS drawing set… now you will have specific interior elevation drawings.
Let me know if that helps!
Mike