Make sure your filters are clean and run what's in it. If the stuff that's in there now has algie growth in it, you can drain and refill all day long, you can steam clean the tank, and it will come back, I've seen it happen more than once. If your worried about algie growth in the fuel get an algecide like Bio-Bore to put in the tank, and several sets of filters to go with it.
I haven't figured out why people think that the algie will hurt the injection pump or anything else downstream of the filters. The filters are there for a purpose, and the media in them are sized for a purpose, and anything, be it algie particles, debris, etc, etc that would pass through the filter normally shouldn't be a problem. The biggest concern with the algie is that it will clog a filter really quickly and cause it to rupture if let go too long. Personally I've seen a sock filter that was origionally close to three feet long pushed/sucked down until it was less than a foot long when it became clogged with the stuff. At that time the machine was crossing a road and blew the O ring gasket out of the bolted on ends of it's housing, shutting the machine down where it sat. This machine had just had the tank (about 200 gallon) drained, opened up, and steam cleaned, because of algie, less than a week before this happened.
Once a tank has been cleaned out and had fresh fuel put in it, along with a biocide, the stuff will still try to grow back. The good thing now is the biocide can now kill just the new growth instead of a whole tank full of the mess. That's why you always need to keep a few sets of filters handy because the dead algie will still clog filters as fast, or faster, than the living stuff will.
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