Since RDF dumps are sharded, resulting dump contains multiple wikibase:Dump schema:dateModified statements. When starting Updater anew from fresh dump load, it bases its starting point on schema:dateModified for dump, however since there are multiple ones, it can choose wrong one (too late) and miss some updates.
The fix for it can be twofold:
- Make Updater use only the earliest dateModified statement
- Make Munger filter out the extra ones (maybe remember the earliest one and drop ones that are higher).