If you have had water in there at the bottom of the tank and it has been sitting with just 2 bars, you've got air in there as well - perfect conditions for rust. When you do the fuel filter, check the condition of the pump.
Make sure you read the posts on replacement parts and hoses. Some are known to have tubes that should not be kept immersed in fuel or in E10 fuel.
It would be prudent to replace that short, thick hose and clamps which join the upper and lower tanks. Make sure you get the correct part for your A9. The design changed with the A8 and later models.
The water drain hole takes water from the left hand side of the filler cap cover ( so it drains when the bike is on the side stand) and feeds it through a metal pipe on the inside of the metal fuel tank. The pipe emerges at the underside of the rear of the tank. There are three tubes that emerge there, which can be seen when you lift the tank. They all have rubber tubes clamped to them. There is a join in the rubber tube at the front left of the seat frame, accessible when the side panel is removed.
Two of the rubber tubes drain behind the sump on the left hand side if the bike - near the gear lever - so they can also get blocked from road muck kicked up by the front tyre.
Having read one post on here about the metal tube rusting through and allowing water to seep in and fuel to seep out, I now make the drain hole part of my regular service schedule. The filler cap doesn't seal the drain hole so when your bike is outside in all weathers water will easily get past the gaps in the aluminium fuel cap, and it needs to flow away. Otherwise when you open the cap, it allows the water into your fuel. It sinks to the bottom of the lower tank, where the fuel pump sucks it up.
So I blast the tubes with compressed air from the pipe at the rear of the tank, refit the rubber tube, clamp it off and fill the metal tube with ACF50 - a penetrative protective 'oil' - and give it time to soak into any rust that might be forming inside, and then drain it out. ACF50 is expensive, so I collect it and reuse it for brushing on other parts that are exposed. But I guess that any oil is better than doing nothing. ACF 50 penetrates well though.
With all of the sand and dust from the Sahara that has been raining on us in recent weeks, These drain holes stand a good chance of becoming clogged with silt