I just installed the new software upgrade on my HPX500. I use a new E-series 32Gb P2 card and ran some tests. Of three takes I recorded, two of the clips lost audio. One was completely silent, the other regained audio on the last second. I recorded nat sound from the front mic. I was just doing tests of the card to FCP transfer, so I didn't monitor the audio and the period between each take was a second. I did not fiddle with the audio controls.

Has anyone had issues with the new E-P2 cards dropping audio? Now, it could have been a mic problem. I recorded audio again, this time closely monitored and with a proper shotgun mic, and the audio was fine.

Most likely it is your audio connector / mic problem. It seems VERY unlikely to be the E-P2 card that is causing this problem.

Of three takes I recorded, two of the clips lost audio. One was completely silent, the other regained audio on the last second.
With a digital recording, you should be able to tell the difference on the audio meters of the NLE between a clip with absolutely NO audio and one where the mic just isn't connected. (You can see the noise floor at a very low level on the meters, typically about -60dB or less.)

I have five 32GB P2 cards (E series) and never have a single problem with audio or anything else.