Since I am not that familliar with PROC NETFLOW I will just keep my comments to methods to deal with this in the traditional NA method.
If your network is simple enough, which it sounds like it maybe [i.e. every path experiences the same loss rate] then you can "Gross Up" your demand [i.e. if you know each and every path is going to have a 3% loss and your demand is 100 then adjust your demands to [100/0.97]=103.0928
However, a more robust way to do it is to have each path have a dummy sink which is constrained to demand loss from the main connection, this way it doesn't matter if the rates are diffferent. The idea being each real line flows to two sinks, 97% to the real one [consumer] and 3% to the virtual one [loss]
Just some thoughts,
Ike Eisenhauer