SAK9, it appears you got conflicting results and I'm in the minority. I agree with others that energy expenditure will be slightly higher. The safety of continuous BSL-3 containment would outweigh that cost, in my opinion.
The parallel operation is a viable option and is a common design today for BSL-3 exhaust systems.
The last three BSL-3 systems I've commissioned all had the configuration of dual fans wyed off a common duct, re-converging into the same stack at an angle that promotes discharge out the stack and not backfeed to the other fan. Each fan is equipped with either one or two low-leakage isolation dampers that close upon fan shut down.
The two fans operate in parallel to maintain a common suction pressure in the duct. The stack's discharge cone is sized as per ACGIH (target about 3,000 fpm) based on the design exhaust volume from the space. If the space exhausts a known, constant volume flow, the plume velocity is maintained regardless of whether one or two fans are used to maintain duct static pressure.
If continuous, uninterrupted exhaust flow from the lab is NOT necessary, the same configuration, or a system with separate stacks, can be utilized with a single fan in operation and the other acting as standby. Then (as suggested above) periodic changes in lead/standby is recommendable to even ware on the fans.
As also suggested above, a strobic system could be used. If the exhausted volume from the space does not vary, however, the strobic system is not necessary.
I'd be interested to know the activity in the space and the designated biosafety level. How critical is maintaining continuous exhaust?
Regards, -CB