Deleting a line scrambles the whole chart

I have OmniGraffle Pro 5, but the problem persists in regular version 6.1.2.

I have a chart with a few hundred boxes with text. Info attached to most items.

I have lines connecting many of the items and most lines are either vertical or horizontal (more or less). If I delete a line, the whole graph gets scrambled. Looks a bit like a spider web. Undo does bring it back, but I want to delete some lines.

I created the chart in v5, so thought I’d try opening in v6 but the problem persist.

Thanks for any help. I wrote support about the problem too.