There have been big issues with LR2s that the battery drains down slowly on. As voltage gets low, some modules are not able to communicate, which can cause them to do strange things.
What ends up happening is the vehicle will enter Crash Mode due to the lack of voltage, and different modules getting 'confused'. This is not an issue when all power is removed, such as disconnecting the battery, as there is no communication at all then.
Crash Mode sometimes requires a reset with dealer level diagnostic equipment, also sometimes resets itself, and there is a procedure(which I have never had actually work) that involves ignition cycles and remote lock/unlock cycles.
Crash Mode is set by the Body Control Module, and stored in the PCM. Sometimes you can get lucky and the BCM will 'unset' it, but it will still be stored in the PCM, and prevent engine cranking. In this case, clearing fault codes with even just a generic scanner will do the trick.
There is a software update to the BCM available to prevent this, however it is usually only preformed after it has been an issue.
Lastly, there have been several starter motor failures, but this should not coincide with a dead battery, but I would suggest making sure that the battery has actually failed, and was not replaced due to a separate no-crank issue.