Thanks everyone in this string for your advise.
How did I solve it, well......over the last days, thinking about how to tackle the problem.
One by one I deleted them, updating the model, trying again and again...... then I didn't have any left to intersect. Not ideal, and lots of time wasted and back to square one, to start again.
Yes please Nemetschek, can we have a bit more of clue to tell us where the problem is when a problem occurs, not just tell us that there is a problem, its just soul destroying...... :-(