The workflow for updating patches from newer kernel:

Diff mainline/ and lttng-patch/ directories. (diff 1)
Diff lttng-patch/ and lttng-module/ directories. (diff 2)

Pull the new headers from mainline kernel to mainline/.
Copy them into lttng-patch.
Apply diff (1). Fix conflicts.

Copy the resulting files into lttng-module/.
Apply diff (2). Fix conflicts.