No a common practice in my neck of the woods, typically the make up (street) water, goes through the filters,softener and to the condensate receiver. I wouldn't put raw,untreated water in,and wouldnt pipe it directly into the boiler for the obvious reason.
Thats a great point that for some reason I overlooked. But true that I am dumping "untreated " water into the boiler. Although Im sure it is not there long before it is "diluted" with the treated makeup.
Your right but the problem wasn't the flood was it? It was after the flood when they drained the system and refilled it. Or did they even put any water back in the system. Maybe not a air problem maybe not enough water. Could be a number of things maybe need more info about what all they have checked and done.
The supply lines may have low points where condensate collected many steam systems are not the same as the original design and changes cause low points that are only noticeable when the system floods. You could try to increase the pressure to blow by these points. This is one of many logical possibilities that could cause this type of problem.
One other point and something I am dealing with now at a location. The air vents at some time were capped off and in order to heat the building the pressure was increased from 1.5 lbs to now nearly 5 lbs. We are in the process of uncapping these vents which should allow for a lower pressure in the system etc. Old steam systems are very tricky.