Every time I use CCleaner I have to get a code sent to my phone in order to get to my emails. Is there anyway to stop this otherwise I just have to delete CCleaner?
as far as I know this is not ccleaner's usual behavoir (to invoke a 2 factor authorization) did you get it from ccleaner.com
Assuming that this is CCleaner on your PC, (and not CCleaner for Android on your phone).
Firstly you need to use 'Custom Clean' and not 'Health Check'. (You can't change what Health Check cleans).
Next:
If you are using an email client (Outlook, Thunderbird, etc) you need to 'Exclude' the email clients app from being cleaned by Custom Clean.
If you are accessing your email through a browser (webmail) then you will need to make sure that Custom Clean is not clearing 'Saved Passwords' and/or 'Session' for that browser. (Untick them for that browser).
In both cases you should also set Custom Clean to 'Exclude' any cookies being used by the email.
Maybe easier, but less secure:
You could check your email client/webpage login to see if you can turn the 2 Factor Authentication text messaging off, but of course doing that leaves your email account less secure. (And you would still need to login each time, but that's more secure than staying logged in all the time).
TBH there is not much point in having 2FA enabled if you are going to stay logged in all the time anyway.
(Although there is a reason for doing that it's less than half the point of using 2FA).
A point to note is that for security/privacy reasons certain apps do not allow you to stay logged in, often email, banking, utility accounts, etc.
They will automatically log you out after a certain time inactive.
So you have to login to them everytime you use them, using 2FA (text message) if you have it enabled.