The days of CCleaner being of significant value are passed. I'd ditch it if I were you.
Or at least, don't run it for a month and see if Armageddon strikes.
It is quite possible that CCleaner is doing this to you if it is deleting the wrong cookies. I know Car4Play used to get confused for me under similar circumstances and only logging in and out would fix it.
If a cookie is harmful you should worry more about stopping it getting on to your system in the first place rather than removing it some time down the line.
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