Can 2 boost converters outputs be put in parallel at the same voltage?
I know this is an older post, but I wanted to mention that parallel sources like this do not inherently split the load current very well.  Supplies are often paralleled in commercial power systems but they have circuitry built in to evenly split the current demand between all supplies.  There is often an extra connection between each supply that allows the supplies to match voltages very accurately and thus supply currently evenly.  It's true you can do OR-ing diodes, as they are called (they work as a logical OR function) but as you already said, this causes power loss, and it still does not result in real sharing.  Sometimes this is done for simplicity in redundant systems where either supply can handle the load independently, in the case that one fails. 

At minimum, OR-ing diodes are a good idea, but if you consider the topology of a boost converter, it has a diode inherently in the design.  I don't think you would get reverse currents when one goes dead.  If you aren't bothered by the fact that one battery would likely go dead before the other, then maybe this scheme could work.  There could be efficiency tradeoffs in some ways also.  I think you will get overall worse efficiency at low load conditions, because you will have two converters switching even if only one is needed.  There are losses in switching converters any time they are switching the inductor.

One last note for the future, 3.3V is really suited well to running on Li-Po and a lot of devices are coming with Li-Po charging circuits built right in :).