Wow, you must have nuked the pool for a long time. We do not "shock" our pools, we follow the SLAM Process when there is a problem and that includes a higher level of chlorine for only 24 hours to get rid of the mustard.
I see you have your pool information in your signature, but we also ask for your location in your profile as location can affect answers to questions.
I have not had any battles with algae yet (Knock on wood!). You need a good test kit and keep track of your chlorine levels (both free and combined) as well as your stabilizer (CYA), PH, and alkalinity (TA). With this information you can calculate your target chlorine level. Stay in this range and hopefully you will not have algae problems to begin with. I find that managing PH first makes hitting all of the other target levels easier.
At the time my cya was over 100 so I brought it up to 40 ppm. I have since dropped it down to 30 but I am asking theoretically in case I need to slam in the future.
But you are just throwing darts if you don't know your pool chemistry. I'm sure someone much more knowledgeable will come along and answer your question if you post a full set of test results.
I am not sure how to say it any differently than has already been said ....
The safe FC level is a function of your CYA level.
At shock level according to the FC/CYA Chart, there should be almost no risk of fading your liner due to the chlorine.
Now if you keep your pH too low, that could also fade the liner. There was also a thread where we suspect the liner was defective and it faded for apparently no good reason.
Follow the chemistry recommendations you find here and your liner should be fine.
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