Neil, you will have to do a lot more than just replace the filter, the whole system will need treating. Its not an ethanol issue, diesel bug has been around a long, long time (its the Supher in diesel that used to keep it at bay, ethanol is an issue in petrol). Its just more prevelent nowadays. Best get a stock of filters in, and drain the water from your fuel tanks regularly. There are threads on here about how best to treat it. My company has spent vast ammounts of money on plant that treats fuel as it is delivered from road tankers to our storage tanks.
BTW I believe Soviet fuel stockpiled for years and then released onto the market after the cold war had all sorts of nasties in it, having been stored for so long.