Static file version information is missing in the real-time data feed

I was developing an application that analyses GTFS-R data feed and last week I encountered an error where my results differed from the operator's real-time app. At first I thought it was my code, but after many hours of testing I discovered that the public transit operator had just updated the GTFS static files (e.g. trips.txt, stop_times.txt, routes.txt etc.) for the winter schedule.

I went back to the GTFS-R specification and I could not find any information about how static file versions are provided within the real-time data feed. I would have assumed that this vital piece of information would be recorded in the header section at least to allow apps an automated means to check that it is using the correct file versions.

Is this correct?

If so, maybe this needs changing, or have others implemented other automated steps to let your app know that the static files it is using need updating. How does one know how to handle the transition or swap over day. Does one just have to assume that the version you've just downloaded is the same one the GTFS-R is using etc.