Flow sensor help

I am looking to inject a fluid into a vessel under vacuum. One of my mechanical engineers is concerned I can't accurately measure the fluid with an ultrasonic sensor while the vacuum draws the liquid. The liquid is pulling from a pressurized canister while my reservoir is under vacuum. Could he be correct? I have included a schematic of my proposed system.

You didn't specify what kind of ultrasonic sensor. I have no experience with in-line transit time ultrasonic flow meters, but some experience with clamp-on transit time flow meters.

The energy pulses used in ultrasonic instrumentation use frequencies above audible audio frequencies and that energy needs to be carried through a medium, gas or liquid. The medium and its characteristics, density, temperature, chemistry, determine the energy pulse's sonic velocity that is used for calculation of the process variable: medium's velocity.

It's commonly known that transit time ultrasonic level sensors on a closed liquid vessel with a vapor space at pressures less than atmospheric pressure do not work because of the low density of the gas medium above the liquid or the lack of medium in which to carry the energy pulses. That might be what your associate is alluding to.

For liquid velocity, clamp-on transit time ultrasonics normally don't care about pressure because the measurement is made from outside the pipe.

But, transit time technology does not like bubbles in the liquid medium; bubbles reduce signal strength. If a liquid medium boils because of low pressure, the boiling bubbles will likely cause transit time ultrasonic technology to fault and not provide a valid reading.

Is the liquid likely to be 100% liquid at the measurement point?
if the fluid remains in same phase it should be OK, if evaporation/bubbling happen due to vacuum it will not be accurate, I guess you may measure the flow before the liquid is vacuumed with the aid of strainer/ valve.