I really don't think it's going to make any difference; remember that modern Lithium Ion battery life is basically based on the number of charge-discharge cycles, which will be the same regardless of how you run--what goes down must go up. In fact, taking the battery out and letting it self-discharge over a period of time instead of float-charging it is going to add charge-discharge cycles, reducing battery life.
Besides, if the PBs work like most similar systems, the DC adapter is probably floating the system power bus when it's plugged in, so you're not exactly "running off the battery", but running in parallel to it so there is no distinction--the power is coming from the adapter either way. The only distinction is made by the battery's internal charge controller to limit incoming current when the battery nears full.
There's no such thing as charging a battery and running off of it at the same time--you have a bus at a given voltage, and power will come from where it can come from. If the current being supplied by the wall adapter is higher than the demand of the system (which it is, or the battery couldn't charge while you were running), then current will flow into the battery, period. If the current coming from the adapter at that voltage were less than the system demand, the battery would pick up the slack--that's the definition of a battery. But unless your power adapter is malfunctioning, that's not going to happen, so you can safely leave the thing plugged in and let it do its thing.
