Battery flat, boot locked
 

Having read about it happen to others it finally happened to me!
I experienced the amazing feature of Audi design, where if the car was locked with the key fob and the power supply is cut off, you cant unlock the boot physically with the key.

It was my fault really, I kept using the Webasto heater for 25 minutes before each day's driving, and I guess with the cold weather and everything the little lithium battery just was not getting charged enough after all that heater use.
So I finally pushed it over the edge and caused the low voltage cut off to kick in. Came back to the car and no power.
The battery low voltage cut off is an ingenious system with one flaw (due to being in the boot). The battery circuit switches itself off to keep enough capacity to start the car.
All you have to do is press the ‘on’ button :D
I could unlock the driver’s door manually and all the other doors. Luckily I have a ski-hatch with all the stuff removed. Using a wooden stick I managed to pry open the battery compartment door.
Still couldn’t see the button. So I taped a small mirror to the stick and moved it around until I could see the battery ‘on’ button. But how do I press the button? I decided I need a L-shaped stick long enough to reach the button. Luckily I had a cheapo metal broom stick with a plastic end and a hole to hang it up. Fishing around for something to jam into it to make a L-shaped stick I found an old plastic compass with a plastic screw-on cap to hold the pencil. So with a bit of fiddling this formed a ‘finger’ at the end of the broomstick to press the button.
After several tries (you have to hold down the button for a second or two to turn the battery back on) I managed to do it, pressed the key fob unlock and the boot opened.

Phewwwwww!

Now I know what a nightmare it must be to have the battery die and unable to open the boot. What a stupid design feature!

This cutoff and "on" button is presumably a feature of your specific lithium battery?

You deserve the Inspector Gadget or McIvor (was that his name?) prize for that Goran! +++

The lock will be seized, should be able to free it off with some WD40 (and some force, or strip and clean depending on your approach) and then use it periodically and problem solved +++

Indeed, there is a direct mechanical link from the lock barrel and, AFAIK no "deadlock" mechanism.
Sounds like you have some sort of mechanical problem that needs investigating, probably in the lock barrel or linkage.

Almost certainly the barrel - my previous fix on a number of Audi's involved a good dose of WD40 and some brute force on the key (mole grips) - goes with a crack and then it works fine afterwards. Risk of that approach is snapping a key - less risky approach would be to strip and clean the barrel +++

That's odd, because when I locked the car manually after removing the battery for a bit of home charging, I could lock and unlock the boot easily with the key.
I hope I wasn't just being thick, but the key definitely would not turn in either direction just after the battery went flat. When I have some time I'll try to re-produce the problem I am now curious what the boot actually does in a power loss situation.

The low voltage cut off is a feature of this particular battery, but I vaguely remember seeing some such add-on circuits for Lead acid starter batteries too.

I'll take that McGyver award thanks :D +++

Was it cold and just frozen?
You need to turn anticlockwise then a bit further and then push in to open.
Alarm will probably go off too, though with the battery "hibernating" who knows...

It was not frozen. The key would literally not budge in either direction.
Then with battery removed, locking manually and unlocking manually smooth as anything.

Odd. It sort of suggests you had either a different boot lock fitted to your car at some point, or you were trying to open with the valet (non flip) key, both of which would behave how you describe....