@herizoludovic and I found a very simple way to solve the issue…. were still keeping an eye on our orders but look like it is as simple as this: Clear the PayPal Identity Token field in the PayPal gateway settings (WooCommerce->Settings->Checkout->PayPal).
WooCommerce stock reducing twice seems due to a conflict with both type communication used by Paypal (PDT & IPN) so in our Paypal log we found out that Paypal was sending first the IPN confirmation and then the PDT confirmation which make the inventory to be reduced twice. Looks like having both configured is the caused of duplicate stock reducing in WooCommerce: https://www.paypal-knowledge.com/infocenter/index?page=content&id=FAQ1142&actp=RSS
Discussion about this bug on GitHub: https://github.com/woocommerce/woocommerce/issues/13963
