I do not understand the chemistry of vinyl liner fading so do not know exactly what level of chlorine will start to fade a liner. It has been written elsewhere on this forum that low pH does more to damage and fade a liner than chlorine, but obviously very high levels of chlorine can bleach dye out of most anything (as several pieces of my clothing with spots on them will prove -- I never wear anything good outside anymore when I dose with chlorine, no matter how careful I am).
Now that said, your CYA level of 40 will tie up most of the chlorine and in theory this chlorine tied up (combined with) CYA should not affect your liner, but I can't be certain of that.
I also do not know definitively precisely what level of disinfecting chlorine is needed to kill this mustard/yellow algae. It has also been reported elsewhere on this forum that using a polyquat algicide will help kill this stuff though generally the philosophy of this forum is to use chlorine whenever possible and save the extra chemicals only when needed (and this may be one of those times).
Refer to this chart and notice that to get 1-2 ppm of disinfecting chlorine (at a pH of 7.5) that appears to be needed to kill this algae, you would need (at 40 ppm CYA) somewhere around 25-35 ppm FC. Keep in mind that this will only give you the equivalent of 2-4 ppm FC if you were not using CYA, but again I do not know if this would damage or fade a liner (my guess is that it wouldn't if only exposed over a week or so -- a year, well maybe).
If you want to play it safe, you could try the polyquat algicide to see if that helps, especially if you are concerned with your vinyl fading. I personally don't think you'll run into a problem with the 25-35 FC level, but then again I don't have a vinyl pool nor your situation. If you do decide to go the "chlorine-only" route, start out at 25 and slowly work your pool up to 35 only if needed and please let us know what happens.
Sorry I'm not more definite about this.
Richard
P.S.
Your web-site is really nice!
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