Recently upgraded from Mavericks to El Capitan. Just noticed that if I 'Clear History', it not only clears the websites that I have visited, it also deletes the sign-in and passwords as well. Is this some sort of security change? In Mavericks I could clear history and it would just eliminate the web sites I visited and not the sing-in or passwords.

Safari does warn you about that if you click Clear History (and thanks for pointing this out; I have never done it). A quick look at OnyX shows that that app allows you to clear History separately from other things. I don't know if that will delete logins and passwords as well, so your on your own. Use the Cleaning tab and select Internet.

This annoying change was ushered in with Yosemite. However, there is a relatively simple workaround. (Note: I'm using Safari 9.0 in Yosemite, but I suspect the procedure is the same for El Capitan.)

From Safari's History menu, choose Show History. In the window that opens, you can clear individual entries, a day or days, or your entire history. See How to Clear History But Not Website Data in Safari 8 for more details. Note: on my Mac mini with 4 GB of RAM, clearing weeks' worth of history ties up Safari for quite awhile; it's clearly a memory- and processor-intensive operation.

that's happening on Yos also isn't it? It's a safari thing more than an OS thing?

Thanks dkmarsh, greatly appreciate the workaround. I just Cleared History and it took me a couple of times to connect the dots when I realized all my other website data was cleared too.