I've recently upgraded EE from version 2.7.3 to the latest 2.9.2, and CartThrob similarly from 2.3.6 to the latest 2.6.1.
All functionality seemed to be fine, aside from my SagePay checkout, which initially fired a 5006 error. I narrowed this down to an issue with extload.php (commonplace!) which I amended by utilising my old extload.php.
There are no obvious errors logged, but I noted pretty instantly that the email notifications (for admin and customer) are no longer being sent; the database does not even log attempts to send the emails. I've confirmed that the backend still has the same email details present, and even tried adding a new, standalone rule that used a non-domain email, in case of any block from that point of view.
On investigation, I've also noticed that after Sage redirects back to site (order complete), the basket retains the items from the order - it previously did not. This even skips the first layer of out of stock warning, allowing items in the basket that are OOS until the point of checkout (where it does then catch them).
Any advice would be greatly appreciated - I've read on similar errors, but not a concrete solution as such. Thanks!