Well even the 600ex flashes with battery packs stopped working at really bad times which is annoying because if you have them all linked and one stops working then they all stop firing.
Mine will fire if one of them has dead batteries. In the photo my set-up was 5D3 with ST-E3-RT and two 600RTs. One 600 set to group A, and the other to group B. In the photo one flash did not fire because its batteries were almost toast, but the other flash fired.
What I'd like to know is: if you have a two or more flashes in the SAME group and one unit has dead batteries, will that affect that group only? I doubt it will as the system is radio.
I have mine set up into three groups. A is on my camera set to ETTL. B & C are my other two flashes on stands. If A, B or C "overheats" then they all stop firing until I turn that group off or switch the power on and off. If I leave the power on the flash will never recover. Switching the power on and off seems to reset it and is is good to go usually for 1000+ more shots. I often take 2000-3000 shots at a reception so they get used quite a bit. I did the same thing with the 580exII flashes and pocket wizards without any problems. I can't do a side by side test because I sold my old 580ex II flashes.