We run a manifolded Acetylene system at our shop and it does have shut-offs for each bottle as well as reverse-flow check valves and flash arresters. Best choice: operate the system as it was designed to be run, with all bottles connected.
If we run less than the number of bottles that were designed into the system we shut off that particular feed and we also leave the empty bottle attached and turned off (if you did have a hiccup in the backflow preventer you wouldn't want acetylene coming from other bottles and feeding into an empty one should the valve inadvertently be left open) and also WELL IDENTIFIED as "empty". The main reason not to disconnect and leave the "pigtail" open is to prevent contamination to the system. Yes the theory would be that the reverse flow would prevent loss of product, but that doesn't address possible contamination that would likely occur. How you address this is certainly your call, however, I would error on the side of caution and safety. Best regards, Allan