Recover/ repair the SharePoint site in IIS on one of the WFE
First stop or move the WFE out of load balancer, then check to see if the path exists under C:\inetpub\wwwroot\wss\VirtualDirectories\WebAppName> it will be the same path on your other WFE, if the folder is still there then open Internet Information Services (IIS) Manager > Right Click on the Site > Manage Web Site > Advanced Settings > Physical Path > and browse to the folder and click OK > Then OK again > IISRESET..
If this is the only issue with the Site, you can copy the folder from the second WFE to the problem WFE and run IISReset. If for any reason you are still having issues, you can disconnect from the farm / configdb and then reconnect to the farm / configdb and all of the WebApps will be redeployed, sites rebuilt etc... However, I don't know what version of SharePoint you are running, if you are running SharePoint 2007/2010 this should be all you have to do..
Disconnect from Farm:
psconfig -cmd configdb -disconnect
Reconnect to Farm:
psconfig -cmd configdb -connect -server "SQLServerName" -database "SharePoint_ConfigDB" -passphrase "passphrase"
psconfig -cmd services install
psconfig -cmd installfeatures
psconfig -cmd secureresources