Does "not provided" affect the referral traffic data?

[devonkrusich]

There is a discrepancy between what an referring site is showing as clicks back to my site versus what Google Analytics is showing.  For example - They are stating that their site sent 100 clicks to my site.  The GA data shows 25 referred clicks from that site.  Could this be due to the "not provided" that hides most of the keyword data?

[Hutch42]

No, not provided is only part of organic traffic that does not pass a keyword.  Any referral traffic you are getting will be shown in the referral section. There are a lot of reasons why what a site reports they sent and what GA sees are different, you should never expect them to line up, but with the difference that you are seeing you should check your GA installation to make sure it is done properly then ask what the other site considers a "click" as many automated functions like spiders will mimic a click, but GA does not track them as they are not people.