How do we handle a situation where the flow reported at a downstream flow monitor is greater than the flow reported at an upstream flow monitor?

We call this situation a flow imbalance, and this is indeed a problem. This first thing to do is evaluate the data from each flow monitor. Were both monitors installed where you think they are installed Are both flow monitors configured with the correct pipe shape and pipe height Is the silt value correct These are some of the obvious things to check. You also need to evaluate the site hydraulic conditions. Are hydraulic conditions optimal at one location and not the other If so, be more suspicious about the location with less-than-ideal conditions. If you find that the monitor data appears in good shape, recheck the mapping and verify that the correct flow schematic is used. If that checks out, you may have to do some field work to further validate the actual connectivity and determine if the maps are accurate or not. Sometimes, a simple error is found, and the problem is easily resolved. Other times, the answer is not as obvious and may require cooperation from the utility, the consulting engineer, and the flow service provider to resolve.