Would a transformer protect a 24V digital flow meter if it received 48V?
It's impossible to say.  It really depends on how the meter's internal power supply works.  

Being electronic, obviously it runs on DC and not 24VAC.  They're just using that voltage because it's extremely common in North American homes, being used as control voltage for the furnace and there's usually an existing 24V transformer somewhere in the house.  Those transformers are cheap and common, by the way; I'm surprised you have to wait for one.  Any HVAC supply will have them, maybe even a hardware store or big-box. 

So it must have an internal power supply. If it's a switching power supplY, they open and close (switch) a gate, and on higher voltage they simply close the gate sooner.  (That is how many consumer electronics can auto-range from 90-264VAC).  So you can run switching supplies beyond max spec if their insulation is in good enough shape to handle the higher voltage.  Insulation is cheap to add to most components (not electrolytic capacitors), so you have a fair chance.  If it's fried and you want to attempt component repair, start with the big caps. 

None of this will fix anything else that was plugged into that 240V receptacle.  



Putting 240V on a NEMA 5 120V receptacle is simply outrageous.  And needless - they make receptacles for that.  They look exactly like standard receptacles except they are keyed differently.  Every big box store and hardware store sells the receptacles and plugs.  



Now if you found a NEMA 6 receptacle and altered your transformer to fit, that's on you.  But if the previous homeowner fit a NEMA 5 receptacle because he was too lazy and cheap to get the correct NEMA 6 at the hardware store, and his logic was "well I know it's wired 240V", then he should have disclosed that in his disclosures, and he would've been written up for it and had to fix it, presumably by installing a NEMA 6.   If he did not do any of that, then he is liable for all your damages here.  I would go after him for it.  Not least, he sorely needs an education, because you bet he did it again to save $5. 

This could have caused a house fire.