Yes, that has always been an annoying 'feature' of PADS. I recently learned on this group that PADS defines the nets as pin-pairs, so when you delete the component you break the pin-pair so PADS deletes the other net. This might be a workaround:
- in Logic (or DxD) add a test point to the net.
- ECO to Layout
- Place the testpoint very near the component you want to delete
- connect the testpoint to the net
Now if you delete the part... Will it keep most of the trace, and only delete the traces between the test point and the deleted part? Try it and see.