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Blind NPTH holes in separate drill layer



for a project I need to do a few blind holes which take a center pin of connectors. 
Due to several reasons we do not want a complete drill but a blind drill hole which has a defined depth (z-axis).

The pcb manufacturer can do this but need these (NPTH) holes in a separate drill layer.
Any ideas how to do that best way ? I have the DS PCB v11 as full engineer version.
By the way, it is just a 2 layer board, already complete designed with big size 200x240mm.

I know that there is an option for multilayer boards with PTH drill holes between some layers but the file is now not a multilayer and I am unsure if this feature would be available for NPTH holes at all.

Thanks for your hints,



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