Hi,
For the failed cases you got, it could be related with the tool size or offset value based on the hole diameter, so could you please try -
1. Use a smaller tool or reduce the offset if possible?
2. Or try to do the chamfer on each hole individually to see whether it can work fine?
3. Or to use 2D Contour with checking "multiple depth" (specify the related taper angle) and the desired offset in bottom height
If you can let us know the tool diameter and the each hole's diameter, it could be better for us to know what the problem is.
Thanks
Hansun