flooded battery compartment - now won't start

[schmooser]

1998 2.5 TDi SE Avant

OK guys - found the (apparently) fairly common flooded battery compartment today, discovered it as I got in and tried to start the car with just the loud click from the starter motor and nothing turning. Popped the bonnet to find a lot of water.
Anyway, have syphoned most of the water out, it was pretty full (about an inch from the top) but on turning the ignition still nothing happens. Battery appears OK but got nothing to test it with, voltmeter in dash reads just below 12 volts, other electrics seem fine, headlights etc.
Can't find any reference on the forum to the car failing to turnover after the compartment flooding.
Am reluctant to take battery out to give it a good charge (and to clear out the drain hole)until I can get hold of the radio code which I don't currently have (does anyone know if the 9v battery in the cigarette socket trick works when removing the battery?)

Is there anything else I can try in advance of getting the radio code and removing the battery?

[robj]

Much better to attach a second battery to your leads before removing them from the car's battery - dont interupt the power supply or you will lose ECU info, not just the radio. Better still, leave it connected, and charge with a portable charger.

[schmooser]

I've managed to clear the blocked rubber grommet in the drain without removing the battery (my god was the fiddly!).

Took the lid of the ECU box, and it looks bone dry in there.

Could it be as simple as a low battery? Even though the dashboard voltmeter reads just below 12? Is it likely that while sitting in that pool of water for goodness knows how long (could be a couple of months!) there was a slow drain somewhere in the compartment on the battery?

I may try and charge the battery anyway, anyone know the implications of charging in situ, 'cos until I get the radio code, I really don't want to disconnect the battery unless I really have to?

[schmooser]

Well, after it standing for the day and a blast with the hair dryer this morning, plus an hour or two on the battery charger, it spluttered into life this evening.
First 3 turns of the ignition same thing, clunk from the starter motor and nothing else, then 4th go it kicked in (slightly hesitantly) took it for a one hour drive straight away.
Voltmeter in dash now reading just over 12, so looks like it may have just been a slight loss of charge on the battery?
Anyway, fingers crossed, it's OK, won't count my chickens just yet until it's been fine for a couple of weeks!
Thanks for the suggestions