Try the command below, it works fine on my side.
$r = Get-AzureRmResource -ResourceGroupName "yourresourcegroup" -ResourceType Microsoft.Web/sites/config -ResourceName yourappservicename/web -ApiVersion 2016-08-01
$p = $r.Properties
$p.ipSecurityRestrictions = @()
Set-AzureRmResource -ResourceGroupName "yourresourcegroup" -ResourceType Microsoft.Web/sites/config -ResourceName yourappservicename/web -ApiVersion 2016-08-01 -PropertyObject $p
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