I have Joomla 2.5.7 in my client's server updated recently from 1.6 to 1.7.

I did not make that site but I am responsible for it now. I prefer to make a site from zero.

Now users area clicking on the menu options and when joomla send them to a meta-url like http://iap.pa.gov.br/acervo they get the message 404 The requested URL /acervo was not found on this server.

Would that be because they moved joomla folder from the root to root/iap (name of the site)?

If it is, what is the configuration to adapt to that new folder?