In my experience, from what I've seen and done, you can fly with parallel battery packs as long as they are exactly alike, ie: same current rating, and same number of cells. Now, as far as charging is concerned, well, I charge my redundant setups separately, either with two chargers or one at a time, depending on what I have available. Since I have four field chargers, well, that takes care of the redundancy..
But, safely, I would advise you do them by the each rather than trying to do them in parallel. I is pretty much absolute that they are not exactly the same so there will be some inbalance in the charging if you use something like a Y cable... of course, that's my opinion.
CGr.