If you have a badly contaminated fuel tank you should be able to treat it and not clean it out. Use a shock dose (100ml to 100 litres of fuel) of Marine 16 Diesel Bug Treatment, stirring in if possible. Leave for 72 hours and then add Marine 16 Diesel Fuel Complete at 500ml to 375 litres. The Diesel Fuel Complete will increase the cetane rating of the fuel and clean your injectors and fuel lines. This should enable the engine to run normally without worry. The sludge build up in the tank may take a couple of doses of Diesel Bug Treatment to fully break up and disperse but it is a lot cheaper and easier than removing and cleaning a tank.
Remember that if you do opt for tank cleaning one remaining organism in the system can kick off contamination again so use a regular (100ml to 2000 litres) dose of Diesel Bug Treatment to ensure you never have the problem again.
Fuel oil heating systems
If you are lucky enough to have on-board heating you can get starting problems due to degradation of diesel in your tank. Some manufacturers recommend the use of a separate tank for heating but this is not always possible. One of the problems for poor starting is the loss in performance of the diesel on storage. This can be rectified by using Diesel Fuel Complete at the standard rate (100ml to 100 litres).