Well, probably only I had this issue. Here is my scenario.
I have a SharePoint farm which is composed of two web servers and one database server. There is a SharePoint web application running on port 31000. For some reason, I extended the web application to another one with port number 80 and host head value MyFQDN. Months later, I decided to stop using the extended application, so I configured the host head value of the original application with port number 31000, and stopped the extended one (but not delete it).
Everything was running well until yesterday the search engine failed to crawl. I got this error:
Could not Connect to the server. Please make sure the site is accessible.
Well, you could find this is a common error in the search if you do some investigation from Google. But this time no solution worked for me. As this is my production environment, I have to make it work as soon as possible. So I changed the Content sources from http://machinename:31000/ to http://myfqdn/ and do a full crawl. It worked!
Now I have time to do more investigations. Usually I only work on the first web server to run Central Admin and to check IIS. As usual I opened IIS Manager in the first server and nothing was different. I didn’t know why I connected to the IIS services in the second web server but I did connect. What?! The original web application stopped and the extended one was running! Who did that?
So I stopped the extended application and started the original one in the second web server, then back to the Central Admin, changed the Content sources back to http://machinename:31000/ and did a full crawl. It worked!
This time I deleted the extended web application from the two web server!