Clearance and tapped holes stopped working.

I had four holes that are clearance and tapped they worked perfectly, when I went to reopen the model a couple of days ago those holes no longer render. They give the error "did not regenerate properly: None of the holes intersected a part". As you can see from the screenshot I have previously projected these holes to a different plane with the same hole settings. The sketches on these planes now complain of "Some external references missing".



If I change the hole depth I can see the holes come through the bottom.

The holes work for all other types of hole.  Why have the holes stopped working for clearance and tapped?