Server tech says that JS was added to 4000 of my pages on May 1st from an ISP in Italy. WTF?

Now I have to re-boot in safe mode to let Avast do a complete system scan to make sure my machine is clean before we do anything. How do I re-boot in safe mode?
Tech also said it might be easier to restore my data from back up rather than try to clean all the infected files. I sure as hell don't want to re-upload 4000 html pages. Isn't there some kind of "find and replace" software I can run to find the JS and replace it with nothing?