Hi Jez,
As you pointed out, when you make a change to the project timeline it will take some time to recalculate the dates across thousands of tasks. There are a couple of options I can think of that you could try and see if it makes the process more efficient:
1) As you mentioned, you could split your project into several (maybe group them into a program to keep them organised in the system) and create cross project predecessors across each of the projects so that the overall timeline is synced. Having less tasks in each project will inherently speed up the timeline recalculations.
2) You may want to try the different planning modes and see if one is more efficient for you (auto-save vs manual standard vs manual timeline). This article on Workfront One here talks through the different settings and how it can affect the timeline planning / timeline recalculations. The timeline planning mode was developed specifically to improve the speed of making timeline changes, however I believe that it only works where there are 2000 tasks or less.
Hope this helps!
Best Regards,
Rich.