It seems to me that the 2 batteries plugged into 2 rx ports should be fine even if a cell shorts. If we say you are using 5 cell packs, then a 5 cell pack with a shorted cell will appear as a 4 cell pack (or just a discharged 5 cell pack). Then from the info above, we can see that even if operated for 24 hours, this would have no bad effects.

Therefore in the event of:

A) a cell going open circuit, the second battery would be 'disconnected'

and

B) the cell going short circuit, the second battery just appears to have a very low voltage, and the situation discussed above applies (ie. a very small amount of cross charging)

So I can't see any problems. I've used this setup before on large models, but haven't actually had a pack fail.