My Blog Links Doesn’t Work

I have Installed WP on the site more than a year ago /blog/ using FTP. Blog used to work really well. Recently, I tried installing a Plugin and, there was a Trojan installed and I deleted the whole blog files on the server and uploaded the previous backup files and guess what? my blog links stopped working. What is the solution for this?

Is there a file missing on the server or should I reinstall WP to fix these broken links? Please suggest. Will I lose the legacy of my blog doing so?