So, there WAS a bug in the way that the software charged the internal batteries that, would, in rare cases, cause the keep alive line to pull current, slowly but consistently, until there was no more that your battery could give.
However, with our latest firmware (downloadable from
http://www.dynonavionics.com/docs/support_software.html), this issue has been fixed.
Now, hooking up the "keep alive" line means that your aircraft's battery will occasionally be used to top off the internal battery if it's installed. If your internal battery is completely dead (say, after playing with your EFIS on the ground w/ master off), this could use as much as 5 amp hours off your aircraft battery (in a 12V system) to fully charge the battery back up.
Our Li-ion batteries don't really self-discharge over short periods of time like NiCd or NiMh batteries do, so once the battery is topped off, it should basically stay there unless you operate the EFIS. So with normal usage, you'd expect the battery to be pretty much full all the time and not require charging from the keep alive circuit.
But, if having power taken from your battery is something that you want to avoid entirely, simply don't connect the keep alive line. The battery will still charge whenever the EFIS has power coming to it while you fly.
Note that if you do not have the internal battery installed, you can connect the keep alive line to keep the clock going. This draws negligible power - just enough to run the clock.