I'd also check temps on the lipos - what I'd worry about is IR differences that would make one lipo get hotter than the other.

When I started running 2 pacs in my MTs they were always paired and charged as a single batt. That got old and I started just charging them separately - couldn't tell any diff. The I bought a 3S and paired it with a older 2S that had 100+ runs on it and I didn't see either lipo get any hotter than the other. These were both Neuenergys and 25Cs.

If the C ratings are realistic and not wildly optimistic (inflated) then as lomng as they are close, I would use them. Just check lipo temps, as long as they are same, its time to play!

All the cautions that get tossed around may be a bit overdone.