www.myexample.com/user1 resulting in Page not found

Since yesterday I am encountering a peculiar problem with one of my drupal installations.

After logging off yesterday evening:

When I enter the following URL: www.myexample.com/user1 ==> I get Page not found - The requested page could not be found.

When I enter the following URL: www.myexample.com/=?user1 ==> I see the main page of www.myexample.com with the url staying the same.

When I enter the following URL: www.myexample.com/node/1 or 2, 3,4,/edit ==> I see the main page of www.myexample.com with the URL saying the same at www.myexample.com/node/1 or 2, 3,4,/edit

I have 3 Drupal installations on one server on godaddy. Reason is, I wanted to have different skins for different sub-websites. So my structure is:

www.myexample.com (it's own drupal installation) ==> the one I cannot log onto. It is up, but I cannot log onto it as admin.
-->www.myexample.com/sub-website 1 (it's own drupal installation)
-->www.myexample.com/sub-website 2 (it's own drupal installation)

I started to encounter problems yesterday when I was still logged on. Sometime yesterday evening, I FTP uploaded the Marinelli theme onto my godaddy server (sub-website folder). I noticed that the FTP upload took longer than usual (I use FileZilla). Than I noticed that it asked me whether I wanted to replace a license file, since it already existed on the target server. I answered yes. After the FTP upload, I noticed that the theme folder did not show up under the sub-website theme's folder. I tried the ftp upload again - however, had the same result. I gave up the ftp upload and continued to work on the main website. However, I started to notice the the edit tab of a particular page did not get me to the edit page. However, instead brought me to the home page of the website. For example, if I selected the third primary menu item, it showed me the page content I created. Than I selected the edit tab of the page, which normally would show you the edit page to make changes, however, this would bring me to the home page (node 1). Hence, I could not make any changes. This strange behavior, seemed to have been restricted to page contents, not blocks, etc. After trying to figure out why for a while, I logged off in the hopes to tackle the issue the following morning. However, now I cannot connect as admin at all.

Can someone point me into the direction of how to troubleshoot and consequently correct it.

All my other drupal installations on the server are working well and I can log onto them.