I just swapped equipment profiles a few times on a single recipe and the sparge water amount changed with each size pot/MLT settings, ranging from 6 gallons to 0.49 gallons. I believe BSmith loads the equipment profile settings first, as a given starting point, and then calculates the EE% against the selected grains, etc. The logic being (I think) that these capacities and losses are measurable and largely fixed, so once you know them and account for them, the remaining variability should come from the grist and your process/EE% for each batch.
Within the equipment profile itself, changing the losses does not interactively change the results. I believe you'd have to adjust the equipment profile and then select it again in the recipe.
I ran into a similiar issue when I prepared a recipe to brew outside, hit a snag, and brewed inside instead. Different pots, water needs, etc., and the water math was entirely different. Less water, higher SG, so I added water in the boil to dilute.