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I've had that a bit recently. Even right after my battery was replaced during the car's Annual Service. I assumed Tesla installed a dud battery and replaced it myself, but continued to have the problem. Then I realized what (I believe) is causing it: I keep the fob in my front right pants pocked and in the winter, I often keep my cell phone in my jacket's front right pocket. I'm pretty sure the cell phone in fairly close proximity was causing interference. Once that message appears on the dash, even waiving the key around the cup holders doesn't make it go away immediately. I found if I pressed one of the buttons, the message would clear. Once I stopped keeping my cell phone near the fob, the problem went away and never came back.
I had to call Tesla to get them to remotely open the door.
So far it was a one time glitch.
Were you parked near anything that could cause a large EMF to exist? Large utility power transformer? Radio broadcast tower? These have been known to cause interference as well.
Instead of waving the fob around, just hold the fob under the two USB ports and it will get recognized. That works even if the battery is almost dead. I think I even recall seeing this in the owner's manual.
The cup holders is the place tesla usually suggests. It had no effect.
From page 41 of the manual:
If Model S does not detect a key when you
press the brake, the instrument panel displays
a message telling you that a key was not
detected.
Place the key in the center console cup holder
where Model S can best detect it.
If Model S still does not detect the key, try
holding it against the center console,
immediately below the 12V power socket (see
12V Power Socket on page 87). Or try using
another key. If another key does not work,
contact Tesla.
A number of factors can affect whether
Model S can detect the key. These include a
low battery in the key, interference from other
devices using radio signals, and objects
between the key and receiver.