During a SharePoint migration using On Demand Migration for SharePoint (ODMSP), you initially migrated content to one library / list in the target and later remigrated to a different library / list within the same target site. Unexpectedly, folders and their contents - including newly added files - were moved from the original target library to the new one. Additionally, some root-level files failed to migrate, resulting in errors.
This behavior is by design in the Microsoft Import API.