In order to recreate the SharePoint site (companyweb) that will be compatible with the SBS console follow the next steps:

1. Using central administration delete the webapp(port 987) ,
   
2. In IIS Manager delete the IIS site (SBS SharePoint) and the AppPool(SBS Sharepoint AppPool)
   
3. Recreate the webapp on port 987 using the following parameters:
   
   1. Create a new IIS web site, and then, for the description, type SBS SharePoint (case sensitive!!).
      
   2. Port, type 987
      
   3. Host header, type sites.
      
   4. Path, type C:\Program Files\Windows Small Business Server\Bin\webapp\InternalWebsite
      
   5. Authentication provider, click NTLM.
      
   6. Allow Anonymous, click No.
      
   7. Use SSL, click Yes.
      
   8. Create a new application pool, and then for the application pool name, type SBS Sharepoint AppPool (case sensitive!!!)
      
   9. Click ok
      
4. In Global Configuration, click Alternate access mappings, and then click Add Internal URLs.
   

   Set the following:

   1. In Alternate Access Mapping Collection, click https://sites:987.
      
   2. In URL protocol, host and port, type http://companyweb.
      
   3. In Zone, click Intranet.
      
   4. Click Save.
      
5. Click Start, click Administrative Tools, and then click Internet Information Services (IIS) Manager.
   
   1. Expand the name of the server that is running Windows SBS 2008, and then expand Sites.
      
   2. Right-click SBS SharePoint, and then click Edit Bindings.
      
   3. Click Add.
      
   4. In the Add Site Binding dialog, for Type, click http, and then, in Host name, type companyweb.
      
   5. Click OK, and then click Close
      
6. External access: Click Start, click Administrative Tools, and then click Internet Information Services (IIS) Manager.
   
   1. Expand the name of the server that is running Windows SBS 2008, and then expand Sites.
      
   2. Right-click SBS SharePoint and then click on Edit Bindings.
      
   3. Select the binding with https on port 987
      
   4. Click Edit and select the certificate : remote.<Domain>.com
      
   5. Click OK, and then click Close
      
7. Using central administration -> Application -> Content Databases: Delete the new content database that was created with this new site and add the content database from the backup using stsadm -o addcontentdb -url <url name> – databasename <database name>

If the steps 2 and 3 are not completed this site will appear as offline in SBS Console.

Source of this procedure:
http://technet.microsoft.com/en-us/library/dd548330(WS.10).aspx Repair user access to the internal Web site

http://technet.microsoft.com/en-us/library/dd560621(v=ws.10).aspx Repair other issues in Windows SharePoint Services