Here are some steps for you
a) Access you site through ftp and remove .htaccess file (possibly backup it)
b) Go to admin of your site (wordpress admin) and open permalink settings form
c) set the first option to custom and put the value in text box
/%category%/%postname%
d) save changes and check you front-end for links
e) if proper links visible check one to view if they aren’t returning 404
f) if you see 404 , put this line at the top of the .htaccess
Options +FollowSymLinks
hopefully this will this the issue
🙂