The suggestion from both BRANZ (link above) and the waterproofing company who've done other work here was to either take them out and waterproof around the edges with new flashing added underneath to deal with future leaks (BRANZ "have the window professionally refurbished"), or replace the windows with modern uPVC ones. Sealing the corners may or may not work, and isn't really a long-term solution.
Has anyone been through this before? There was a thread on alu windows a few years ago but that was mostly advice on new ones... I know that in the long term I'll probably have to get them taken out and sorted, but I'm dreading the hassle and mess of removing and replacing them in rooms that have only just been completed after the rebuild.
And finally, to anyone else who has the dark 1970s/1980s-style alu window frames, get the corners and walls underneath checked for moisture. There were moisture problems with pretty much every window I checked here.
Edited to add: Comment from the architect, even if the window is taken out and refurbished it has to be done to a certain standard or may not be able to be refurbished. Refurbs are popular in reclads to save the cost of a new window.
In this case given the amount of work involved it probably makes sense to just put in new windows...