Eliminating 'Negative' Flows

Flow direction arrows are for reference only, the actual direction being determined by the analysis and, if the direction is opposite the reference direction you've specified, values for flow, velocity and pressure drop will be negative. If you don't want negative values, simply select the pipe, press F3 to toggle the direction arrow and rerun your model.

While this is fine for one or a few pipes, what if you have many pipes with negative flow values?

Within the Workspace, open Select Special (on the Edit menu or by pressing F6). For 'Selection Type', select 'Pipe Output Properties', then 'Volumetric Flow Rate' for the 'Pipe Property'. Next to 'Range', input a negative flow value in the 'From' field larger than the largest negative flow in your output and '0' in the 'To' field, then click on 'Select Pipes'. Click on 'OK' and you'll be back in the Workspace with all of the pipes with negative flows selected. Now, simply press F3 to reverse the flow direction arrows of all the pipes and rerun your model. No 'negative' flows.

P.S. You can also Select Special pipes based on negative velocity.