Hope it's okay that I use this thread to inquire about the exact same problem I experienced two days ago. This is the first time this has happened to my site and my web guy doesn't know why.
I have two main keywords I use to rank for my home page and it ranks in the top 5. Two days ago, it went missing. It wasn't on the 2nd, 3rd, 4th, or 5th page, so I used a link operator to check and noticed the home page wasn't indexed at all. I googled my domain name only to see the home page URL with the /index.php at the end of it show up. Why Google indexed that page instead, just out of the blue, is a mystery to me.
But this is what transpired the week before that lead up to that problem. Last week, I transferred my domain from one registrar to Godaddy. I still use the same host, not Godaddy's. The transfer was successful and the site worked just fine after the transfer was complete. The site still retained its ranking. Then two days ago, this index.php shows up in place of my actual home page. Not only that, my home page, which is supposed to be a PR 5 site is now a PR 0. Yet, the few inner pages that also have PR still have theirs though. It's just the home page's PR that is gone. AND, 6 of my main inner pages have been de-indexed as well.
I'm hoping this is a known and fixable problem. My web guy immediately did a permanent 301 redirect from the URL with the index.php to the one without, and I'm just waiting for Google to re-crawl the page and see the redirect. Is this the correct fix to my problem? Because if not, could it be something to do with the domain transfer?
Thanks for any and all insights.