Getting back to this as a documentary step.
I had deleted assets in the content browser (from MSPresets and from Megascans).
Nevertheless, there were remaining .uasset files in each of those folders, which did not show up in the content browser.
After double-checking that there were no more references to those assets, I deleted them via the filesystem .
That’s all there is to it. Obviously, the bundling process iterates over everything in the project folders, finds the assets that have been marked for deletion by git and doesn’t have a strategy for handling those.