All of my links that were in /link/ format are magically broken? now I can only access /?q=link

For some reason all of my links on my Drupal 4.6/ Civicspace 0.8.2 Install stopped working…

All of my links that were in /link/ format are magically broken? now I can only access /?q=link
This used to work: http://mysite.com/user/5
And now only this works: http://mysite.com/?q=user/5

It is almost acting like it upgraded itself or something… The problem is that my Drupal install up to this point has totally been based on the /user/5 method

I cannot even login because when I try to send my information, it tries to post to a http://mysite.com/user/login?destination=user page.

What I did before this was:
Sent email to client w/ username and password of: emily on 7/28.
Site was working properly at this time.
On 8/2 8:30 pm performed the following actions in the following order:
(it is not known if prior to performing the below steps that the link were already broken, as I had not checked since 7/28)
- Removed FrontPage Extensions via Cpanel
- Backed up Drupal Database via Cpanel
- Performed Backup of Home Directory via Cpanel
- Performed Full Backup of all files via Cpanel
- Performed Full Backup of Database via Cpanel
- Created test database via Cpanel
- deleted test database via cpanel
- recreated test database via cpanel and added the drupal user to it
- created test directory and uploaded a copy of existing drupal install to it.
- went to check the /user/ page to login to get to /admin page and realized that it was a broken link, and then realized all links were broken.

I can provide actual url's to anyone that would like to see, please let me know.