Comment 6 for bug 479553

a) manually adjusting a connector end point disconnects the connector end point <http://tavmjong.free.fr/INKSCAPE/MANUAL/html/Connectors-Modifying.html>. What is missing has already been filed many times as RFE: “multiple user-defined connector points” (see bug #171027 <https://bugs.launchpad.net/inkscape/+bug/171027> and its duplicates).

b) the dislocation of the disconnected ends of the connector lines is certainly not expected behavior and has the same root cause as the other bugs you filed with the same octree drawing (excluding so far the original ODG and WMF export issues): clones and connectors inside (nested) transformed groups.

You can verify yourself that it is related to the 'resizing' or 'fit page to selection' transformation that is applied to "Layer 1":
1) open the original octree drawing, open 'Edit > XML Editor', select "Layer 1" in the list of elements on the left
2) in the attributes list on the right side, select 'transform' and use the 'delete' button in the toolbar
3) back in the main window, zoom out to see both the page border and the diagram which has been moved back to its position relative to 0,0 before the page resize.
4) now you can move, ungroup or otherwise edit the groups, connectors and clones without any unexpected dislocations of endpoints or objects.