Let's look at both sides of the discussion. We'll begin with reasons for alternating pumps:
If the pump is not run, the oil will drain away from the movable components, causing excessive wear and heat at startup.
Maybe the standby pump is frozen up. It's too late to learn that when you need the pump.
All standby equipment is subject to vibration. Bearings can be affected by this vibration with a condition known as "false brinneling," causing round, hard indentations in the bearing races.
People that do not believe in alternating pumps also have some compelling arguments:
Every time you switch pumps you are causing a system upset than will probably affect the finished product. Temperatures and pressures change and some products become viscous or solidify when the system cools even a small amount. All of this translates to "off product" that will end up in the alcohol plant, have to refined all over again, or is sometimes shipped to the customer who refuses the shipment and asks you to initiate a program that will prevent this from ever happening again.
Each time you let the bearing cavity cool down you are producing moisture in the bearing case. The more often you start the pump, the more frequently this occurs. Moisture is a major cause of premature bearing failure
Startup torque is five times running torque meaning that it takes five times the power to start a pump than it takes to keep it running. These power surges can trip breakers or, in some cases, cause you to exceed your peak loads that will have an adverse affect on next month's electric bill.
Every time a pump starts the shaft thrusts towards the thrust bearing and then somewhere close to its 65% efficiency point, the shaft thrust in the opposite direction towards the pump volute. This axial shifting can cause seal and bearing problems.
Shutting down a pump will cause its internal temperature to change and that can cause a problem with many fluids. In some instances the shutdown pump has to be flushed out to prevent product from solidifying in the seal or on the surfaces of the impeller and volute. At startup, any of these solids that have not returned to their liquid state can cause the rotating shaft to go "out of balance."
Most knowledgeable people agree that pumps with long shafts should be turned over on a regular basis to prevent "sag." Jacking gear is often provided to do this.
If you decide that alternating pump makes sense to you, be careful that you do not run the pumps for the same amount of time, or they will both wear out with the same amount of hours.