FWIW, after the file was reset, I didn't realize it had been reset, because the logo didn't change on my page, even though I was hard-refreshing. Since the logo wasn't changing but I wasn't prompted for overwrite, that's why I asked you if the choices are cached. But it looks like the old logo, after it is overwritten, is cache, and this is related to #991. Maybe flushing varnish will fix this, but caching seems to be wrong on the dev server.