At Cheddar we use the DoReferenceTransaction
method with a "billing agreement" to enable transacting against a customer's paypal account repeatedly on any schedule for any amount. We have some documentation in our KB regarding how to create the billing agreement token via your app. Section 2.1 of that article would be relevant to anyone getting started with setting up a billing agreement for purposes of executing reference transactions. The rest of it is specific to Cheddar.
We, too, are aware that this method is officially deprecated. Our inquiries with PayPal suggest that it will be supported indefinitely. The new REST api does not support a modern equivalent. In other words, there's no new replacement for the DoReferenceTransaction
method of Express Checkout or any alternative that enables autonomous recurring billing for variable transaction amounts on a custom schedule. If there was, we'd be using it. Practically speaking, there are countless implementations in the wild using reference transactions so I expect it would be impossible for PayPal to stop supporting it without an alternative (new) method.
FWIW, I recommend using a subscription management service provider like Cheddar. There are others that support recurring payments via PayPal account as well. Recurly comes to mind. Recurring billing and subscription management is complicated and it's made quite simple by these services. I recommend against using PayPal's native recurring payments as it is unnecessarily restrictive and once you start using it, you can't stop.