My theory is that there is some shortage due to flooding, which causes battery to discharge and setting off the alarm...

Shortage needs to be eliminated, leak plugged and battery replaced. If battery manage to discharge that rapidly to that low level, it is probably not very good at this point and might have developed some undesirable "features".

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His : 2013 X5 3.5d Deep Sea Blue/Black/Aluminum with ALL packages, 20" 214"s, running boards, Adaptive Drive, Spare Tire, BMW Apps
On Order : 2016 X3 3.5 MSport Silver/Mocha with DHP, CW, Prem, Tech, DA, Lighting

Hers : 2015 328xi MSport Silver/Red

Prior:
2008 X5 4.8
2011 X5 3.5d
2010 335 xDrive
2013 335 xDrive