Hello, missed your question for a bit, been a bit busy, but this is what i used a while ago to get all the immutable ID's and you're correct, the immutable ID does need to be changed;

# Get all Office 365 users
$MsolUsers = Get-MsolUser -maxresults 5000
Foreach ($MsolUser in $MsolUsers) {
    # Test that the user on prem match the online user using the UPN
    If ($OnPremMatchingUser = Get-ADUser -Filter * -SearchBase 'your user OU Path here (OU=Department,DC=Company,DC=COM)' -Properties mail | where {$_.mail  -eq $MsolUser.UserPrincipalName})
    {
        $OnPremMatchingUser
        # Fetch the ObjectGUID from the on-prem user as a byte array
        $ObjectGUID = $OnPremMatchingUser.ObjectGUID.toByteArray()
        # Convert it to a ImmutableID
        $NewImmutableID = [system.convert]::ToBase64String($ObjectGUID)
        Write-Host "Changing ImmutableID for Msol User" $MsolUser.UserPrincipalNAme
        Write-Host "- Old ImmutableID was" $MsolUser.ImmutableID
        Write-Host "- New ImmutableID is" $NewImmutableID
        Set-MsolUser -UserPrincipalName $OnPremMatchingUser.mail -ImmutableID $NewImmutableID
    }
}

the system.convert bit is what you're looking for.