Peter,
According to several other users, the project manager actually ignores nested sequences, unless those sequences are selected by the tick box. Which, kind of makes sense. My problem was that I WAS selecting all of the nested sequences with the tick box, but after more investigation it seems as though the problem was this: if 'Nested Sequence 01' and 'Nested Sequence 02' both contain a clip from media file 'A001C001' then that media file would be trimmed to appear in 'Nested Sequence 01' but would then be ignored for 'Nested Sequence 02' and removed from the trimmed project, with no notification or indication at all unless I manually go through and check every sequence against it's counterpart in the original. This problem even occurs if, I go to each of the clips appearances in the different sequences, create subclips for each of them, place those subclips on the timeline in place of the original, and then convert those subclips to individual master clips. This is extremely frustrating and leaves with me with absolutely no confidence in Premiere's ability to do what is advertised. Furthermore, it's really screwing up my schedule for delivering my work to our VFX artist.
It's honestly really great that Adobe are constantly striving to have the most 'cutting edge' tools, like a project manager that finally contains features that have been included in Avid and FCP for ten years. But I believe I speak for a huge portion of customers when I say that, for the past few years, the updates to Premiere have felt like hopping from one damaged Beta version to the next. Please stop rushing out untested versions of the software with fancy new buttons and just focus on making the existing version, that people are already paying for, work properly and stably.
Best Regards,
Martin
PS. Kudos on successfully taking a complaint about a technical fault in your software and using it as an opportunity to sell me something instead of actually offering any real assistance.