Besides the problem I mentioned here, I'm also recieving spammed versions of the index.html in the main folder used to redirect to the dotnetmuke sub-directory on my site.

I copied the whole ftp site onto my computer and avg found these files to be infected:

dotnetnuke\js\ClientAPITests\default.htm

dotnetnuke\js\ClientAPITests\dnn.dom.positioning.htm

Would simply deleting these files fix the problem? What do they do anyway?