Personally, mine has been clear by keeping the FC up to what the "best guess" level suggested ever since the algae has been dead.
Don't worry about vacuuming to waste. We do our whole bottom (18x36 IG pool) and only lose about 2 to 4 inches.
And we didn't do anything different to the filter, as far as any algae in it. It just wasn't needed for us.
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