I have just fixed my late 2013 retina MacBook Pro from this verry issue.
I too, encountered a dead battery on mutiple occasions after leaving the rMBP to Sleep with ~80% battery remaining, only to wake up the next morning to a dead battery.
I logged my encounters with Apple Support who assisted me as best they could. I reset my SMC and PRAM but it had no effect. At one point, I was convinced that the Diagnostics pointed me to an Address Book Contact synchronization issue that endlessly ran in the middle of the night (log entries showed it attempting sync multiple times a minute for hours on end) until the battery finally reached 1% and shut the unit off. But this was a side effect and not the root cause of the issue.
After encountering this issue of a dead batter at least a half dozen times, I booked an appointment with the Genius Bar. I had backed up using Time Machine before heading to see them and on site, all hardware tested fine. It was a software issue. They then restored the OS back to a clean Mavericks OSX 10.9.2. and asked me to slowly reinstall progams keeping watch for the reappearing battery draining symptoms over the next week. I've since reinstalled all programs and apps that I normally use and had installed prior to the OS restoration with the exception of AVAST (antivirus... i know, i know.. the OS has malware/etc. detection built in.)
My retina MacBook Pro has been going strong overnight on battery with only 1-2% of discharge over 8 hrs. Sweetness!
TL;DR: UNINSTALL AVAST. It's screwing with your software and refuses to allow the rMBP running Mavericks to maintain Sleep, which kills your battery.
I've already logged this with Avast here: http://forum.avast.com/index.php?topic=145533.0
I hope that this helps someone. I know how frustrating it is when a super piece of hardware is brought to its knees by (crap) software.
Tags: retina MacBook Pro Late 2013 Battery Drain Discharge Sleep Mode