Swiss
Did you set the generations of ancestors and descendants to a high number?
I created a copy of my file with 5795 individuals. I opened that file and created an Extended Family Chart but forgot to set the generations of ancestors and descendants to a high number. When I deleted the people in the chart I was left with a mess, unconnected islands all over the place. I created a new copy of my file and set the generations of ancestors and descendants to a high number. This time it deleted all but 36 people from my file. These are two small islands I expected to be left. If you choose to export the individuals in the chart the same rule applies, high numbers.
Curt