As nobody knew an answer, so I started trying rebase strategies (-s, -X options), one by one. Using 'git rebase -s recursive -X ours ...' was the only one which did something useful for this self-rebase and also worked with a mangeable set of conflicts (only ones including a file deletion), so I got away with resolving some 30 conflicts with 'git rm ...'. Now I have a branch with 4700 commits on it, but zero merges. Diff melted down to 3800 lines. That's something I can work with.
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