An opinion based on less than a complete understanding of the underlying problem.
Just to make sure I'm on the same page as you, a center point run is the middle of each continuous factor. In typical DOE coding (-1, 0, 1) a center point is where all the continuous factors are set to "0". The problem is that categorical levels are coded 1, 2, 3..., there is no "0" center. When there are categorical factors, you'll have to decide which level you want to consider the "center", or you might want a center point run for each level of the categorical factor.
Since you have disallowed combinations, it's possible that the center points for all the continuous factors fall into the disallowed range?
Will the model work if extra runs are added? (...or, Will the data still be analyzeable if I add runs that affect the orthogonality of the design?)
1. Adding, manually, center point runs will probably be OK.
2. The Fit Model platform that you'll use to do the analysis works great on both well-structured experiments and completely ad-hoc happenstance data.
Hope this helps.
Cheers,
B
JMP Systems Engineer, Health and Life Sciences (Pharma)