Anyhow, here's my guess at what happened: say your original dag was foo.dag. You did
 condor_submit_dag foo.dag
and this had two nodes fail, producing a rescue DAG:
 foo.dag.rescue.001
>From your description, it sounds like you did this:
 condor_submit_dag foo.dag.rescue.001
and then
 condor_submit_dag foo.dag
Is that right? Did you remove foo.dag.rescue.001 before re-submitting the original DAG? If so, that would explain why all of the jobs got re-run.
If you're using the default settings for DAGMan, what you want to do after the first run fails is just
 condor_submit_dag foo.dag
which will automatically pick up the status from foo.dag.rescue.001.
It's expected that doing
 condor_submit_dag foo.dag.rescue.001
will fail...