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.
How do you set the on-camera unit to group A? I can't seem to replicate your set up (I only have two 600RTs), and the manual leeds me to believe you can't do that. It's the same with the ratios on the flash that's a master, you need to also have two or more slaves to use the ratios. With a flash as a master it seems to be excluded from any group, and any tests I'm doing seem to prove ratios are useless with an on-camera 600rt and a single slave 600rt. With the st-e3-rt mounted on the 5D3 it all works as you'd expect, and works well imo.
Also, let it be known the manual is a lesson in ambiguity. The top of the manual's page 49 seems to back up my claim of ratios not working with a 600rt at a master. Quote: You can divide the slave units into two or three groups and perform E-TTLii/E-TT auto flash shooting while changing the flash ration (factor). In addition, you can set and shoot with a different flash mode for each firing group, for up to 5 groups.
I think there might be a little confusion so I will try it again to see if it makes a little more since. I have 3 flashes. One on camera and two off camera. My on camera flash is set to ETTL master in group mode. I don't do anything with ratios. I know that my on camera flash is set to group A because when I adjust the exposure compensation for that group the flash on my camera is affected. My first off camera flash is set to slave in group B and it is manual set at 1/32 or 1/64 power usually. My second off camera flash is set to slave in group C and it is also set to manual and 1/32 or 1/64 power. I have had all three flashes overheat at various times. They all have very light loads. My on camera flash probably has the biggest load but ettl at ISO 3200 doesn't take much power. Im my opinion all flashes should last for hours on a set of batteries without overheating in those conditions. I can't compare them directly to the 580ex II flashes because I don't have them anymore but I never had that problem with them and I did the same thing only with pocketwizards.