It is critical. In Jena the worst is over, but in Dresden nobody knows. Tonight and tomorrow morning the peak of the flood is scheduled to pass through Dresden. There is no need to evacuate the whole city - the higher parts won't be affected. Some low-lying suburbs have already been evacuated and more might follow. The flood is almost as high as the 2002 one but they hope their new flood protections are good enough to save the city centre. All they can do is hope and pray, and fill and pile up sand sacks and protect their belongings.
You will of course be safe because if there are dangerous areas they will be cordoned off and you won't be let in. However, better contact your work commitments and hear what they say. They might be busy with emergency situation and postpone the appointment ,or at least relocate the meeting to somewhere outside the city centre. They will know best how to estimate the situation.
The trains on your route are currently running normally, perhaps with some delays. Nobody can predict at the moment what's going to happen during the next two days, though.