JP2 is the place where the two sources of current join so that either can power the circuit. JP2 is there so that the feed from the a.c. adapter can be cut off so that the USB supply doesn’t back-feed into that regulator i.c.
As Paul said, it’s advisable to remove the jumper - though I admit I rarely bother - but then I use the emonTx for development and support, it’s not a permanent fixture.