No - the CYA makes the chlorine less effective. Meaning that at a CYA of 100 with 25ppm is equivalent to NO CYA and 10ppm at shock levels. There is no higher chance of your liner fading at either point.
HOWEVER IMO - to be on the safe side I have seen it recommended that a liner pool remains below 20ppm. If your CYA level is higher and constitutes a higher than 20ppm shock level - it would be better to drain/refill to bring down the CYA level so that you do not need to shock to over 20ppm than to accidentally overdose the pool and have permanent damage to your liner.
When you shocked before - were you testing your own water - or was the pool store handing you 6 lbs of stuff and telling you to throw it in your pool? It could be that if you were not testing your water - that your shock level was a lot higher than needed and that is what faded your liner.
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