Its true that clearing cookies should not create any actual harm. But its not something you should just casually do. Cookies are there for a reason. Once you clear your cookies, all of the websites you routinely visit will no longer just let you in, but will require a login. That's a pain. I forget my passwords routinely.
I DO want to make all my amazon's purchases through PSS, but I will not be clearing cookies twice a week. Its like your barber saying that you need to shave your head before each new haircut. Someone in the IT department is (with all good intentions) overestimating the importance of this.
Yes it may be true that you remove any chance of amazon not getting the right affiliate, but at what cost? This is like FAA restrictions on cell phone calls while taxiing. If your phone is turned off, then there is zero chance of crashing the plane from your phone's interference. That is totally BULLSHIT!. ;-)
According to the research i did (and i am NO EXPERT). The reason for clearing the cookies is to make sure that you are forcibly removing the other Amazon affiliate's cookie that may be there. So in other words... if the listener thought he loved some other podcast yesterday and clicked through THEIR link (Rush Limbaugh would call them a whore), clearing the cookies will ensure that PSS gets credit for the next sale.
But then tomorrow, that podcast will tell their users to do the same, and you will get your cookie overwritten... and we're back at square one. Any gains are temporary and, quite frankly, seem to me like cheating. If I know anything about Penn, I know he would not be for that.
Just an opinion. I love the show and the smart discourse i find on this site.
Read this Amazon Cookie Research if you dare (and prepare to get the catch pole)