user cannot access subsite after vps crash

Hi my VPS server self destructed at Bluehost (after their main meltdown last month) and I had to reinstall my entire network from backups. All is good except one thing: users cannot access their sites. At first I couldn't access the network but host support had me re-input the multisite htaccess code and it worked. Simply re-input it and save it and it worked.
My question is this: since I reinstalled my whole network using backups, the database name changed, etc.
But I still have no idea why users can't access their sites. Thanks very much.