I think I found the solution: I dropped the tables piwik_archive_numeric_YYYY_MM
and piwik_archive_blob_YYYY_MM
(where YYYY_MM is the corresponding year/month). After that, the data seems to be regenerated upon the first call.
In the Piwik FAQ Entry "How do I delete all statistics for a given website, or for all websites?" it is stated that "They will automatically be re-created from the Visitor logs when Piwik processes your reports.". However as I am using this for an importer script, I am not sure how this will affect other/existing data - So use at your own risk!