I had an issue with a Small Business Server SBS 2003 to SBS 2008 migration where once everything was up and running, I had problems with Outlook 2007 Clients giving certificate errors.  Also, OWA Outlook Web Access would redirect to http://sites/owa.  The problem was the internal and external URL settings on the various transports in Exchange 2007.  This powershell script helped to fix the problem.  Note, some errors occurred for me but I was able to just step through the code and issue the commands to the Exchange Shell manually to get the job finished.  The main problem was the AutoDiscover Internal URI - once that was fixed the rest fell into place.

# Script to allow you to set all virtual directories to a common name like mail.company.com

Start-Transcript

# Variables

[string]$UMExtend = "/UnifiedMessaging/Service.asmx"
[string]$OABExtend = "/OAB"
[string]$SCPExtend = "/Autodiscover/Autodiscover.xml"
[string]$EWSExtend = "/EWS/Exchange.asmx"
[string]$ConfirmPrompt = "Set this Value? (Y/N)"
[string]$NoChangeForeground = "white"
[string]$NoChangeBackground = "red"

Write-host "This will allow you to set the virtual directories associated with Autodiscover provided services to the name you provide."
Write-host ""
[string]$base = Read-host "Base name of virtual directory (e.g. mail.company.com)"
write-host ""
# =======================================================
# Validate if a third party trusted certificate is being used
# because BITS won't use untrusted certificates
[string]$set = Read-host "Is the certificate being used an internally generated certificate? (Y/N)"
Write-host ""

if ($set -eq "Y")    {
    [string]$OABprefix = "http://"
}    else    {
    [string]$OABprefix = "https://"
}

# =======================================================
# Build the Autodiscover URL and set the SCP Value

Write-host "Setting Autodiscover Service Connection Point" -foregroundcolor Yellow
write-host ""

$SCPURL = "https://" + $base + $SCPExtend

[array]$SCPCurrent = Get-ClientAccessServer

Foreach ($value in $SCPCurrent) {
    Write-host "Looking at Server: " $value.name
    Write-host "Current SCP value: " $value.AutoDiscoverServiceInternalUri.absoluteuri
    Write-host "New SCP Value:     " $SCPURL
    [string]$set = Read-host $ConfirmPrompt
    write-host ""
    
    if ($set -eq "Y")    {
         Set-ClientAccessServer -id $value.identity -AutoDiscoverServiceInternalUri $SCPURL
    }    else {
        write-host "Autodiscover Service Connection Point internal value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
    }
}

# =======================================================
# Build the EWS URL and set the internal Value

Write-host "Setting Exchange Web Services Virtual Directories" -foregroundcolor Yellow
write-host ""

$EWSURL = "https://" + $base + $EWSExtend

[array]$EWSCurrent = Get-WebServicesVirtualDirectory

Foreach ($value in $EWSCurrent) {
    Write-host "Looking at Server: " $value.server
    Write-host "Current Internal Value: " $value.internalURL
    Write-host "New Internal Value:     " $EWSUrl
    [string]$set = Read-host $ConfirmPrompt
    write-host ""

    if ($set -eq "Y")    {
        Set-WebServicesVirtualDirectory -id $value.identity -InternalURL $EWSURL
     } else {
        write-host "Exchange Web Services Virtual Directory internal value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
     }

    Write-host "Looking at Server: " $value.server
    Write-host "Current External Value: " $value.externalURL
    Write-host "New External Value:     " $EWSUrl
    [string]$set = Read-host $ConfirmPrompt
    write-host ""

    if ($set -eq "Y")    {
        Set-WebServicesVirtualDirectory -id $value.identity -ExternalURL $EWSURL
    } else {
        write-host "Exchange Web Services Virtual Directory external value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
    }
}

# ======================================================
# Build the OAB URL and set the internal Value

Write-host "Setting OAB Virtual Directories" -foregroundcolor Yellow
write-host ""

$OABURL = $OABprefix + $base + $OABExtend

[array]$OABCurrent = Get-OABVirtualDirectory

Foreach ($value in $OABcurrent) {
    Write-host "Looking at Server: " $value.server
    Write-host "Current Internal Value: " $value.internalURL
    Write-host "New Internal Value:     " $OABUrl
    [string]$set = Read-host $ConfirmPrompt
    write-host ""

    if ($set -eq "Y")    {
        Set-OABVirtualDirectory -id $value.identity -InternalURL $OABURL
    } else {
        write-host "OAB Virtual Directory internal value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
    }

    Write-host "Looking at Server: " $value.server
    Write-host "Current External Value: " $value.externalURL
    Write-host "New External Value:     " $OABUrl
    [string]$set = Read-host $ConfirmPrompt
    write-host ""

    if ($set -eq "Y") {
        Set-OABVirtualDirectory -id $value.identity -ExternalURL $OABURL
    } else {
        write-host "OAB Virtual Directory external value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
    }
}

# =======================================================
# Build the UM URL and set the internal Value

Write-host "Setting UM Virtual Directories" -foregroundcolor Yellow
write-host ""

$UMURL = "https://" + $base + $UMExtend

[array]$UMCurrent = Get-UMVirtualDirectory

foreach ($value in $UMCurrent) {
    Write-host "Looking at Server: " $value.server
    Write-host "Current Internal Value: " $value.internalURL
    Write-host "New Internal Value:     " $UMUrl
    [string]$set = Read-host $ConfirmPrompt
    write-host ""

    if ($set -eq "Y") {
        Set-UMVirtualDirectory -id $value.identity -InternalURL $UMURL
    } else {
        write-host "UM Virtual Directory internal value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
    }

    Write-host "Looking at Server: " $value.server
    Write-host "Current External Value: " $value.externalURL
    Write-host "New External Value:     " $UMUrl
    [string]$set = Read-host $ConfirmPrompt
    write-host ""

    if ($set -eq "Y") {
        Set-UMVirtualDirectory -id $value.identity -ExternalURL $UMURL
    } else {
        write-host "UM Virtual Directory external value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
    }
}
Stop-Transcript

(http://www.exchangeninjas.com/set-allvdirs)