I've heard of users modifying the Specific Gravity calculation option for fluids other than water, (View > Calculation Options > double click active steady state/eps solver option set) but I do not recall hearing about a need to change anything for water at different altitudes. According to wikipedia, the gravitational constant varies by only .0.04 m/s^2 depending on the elevation.
The only thing I can think of that you would need to change for transient analysis purposes is the pipe Wave Speed (you can account for it using the Wave Speed Calculator Tool) and the vapor pressure limit (default is -9.98 m, as seen in the transient solver calculation options)
Please clarify if I have misunderstood.