A solution could be something like this perhaps?
foreach ($line in $lines) {
$index = $line.IndexOf('=')
$name = $line.Substring(0, $index)
$value = $line.Substring($index + 1)
$value = $value.Replace('"', '')
$name = $name.Replace('__', '')
if ($value -ne '') {
dotnet user-secrets set $name $value | Out-Null
}
}