Something similar happened to us once on a now-gone statuon. Many moons ago when we switched from airing Casey Kasem on CD to receiving it via FTP download the download didn't render. However, since the process had started it had overwritten the show from the previous week so all of the files were empty.
At 8am the Casey legal ID fired off, followed by all of the spots and Casey rejoin liners that were scheduled around the show segments as each show segment file was there, but an empty file that was skipped over. Then around 8:30ish our automation (Maestro) was already playing out the 12pm hour of programming.
Fortunately I was 1) up to listen to Casey and 2) the live jock for the 12p-6p shift. I realized what was happening and showered and got to the station as quickly as I could and played the FTP files over the air in real time for the first 2 or 3 segments while I got the rest of the show loaded into the system, cleared out a few spots that I could move and got the show finished by about 12:20 without skipping over any segments