Some base tables like Note tables do not have user keys. Since user keys play a vital role in migration of data using EIM, the EIM behavior is significantly different in case of Base Tables without user keys.
For such tables, although IMPORT and EXPORT processes work, but Merge process does not work.  The DELETE process, when using DELETE MATCHES and DELETE ALL ROWS parameters, works fine, but does not work with DELETE EXACT parameter. This is because the EIM process cannot identify the rows to delete, in the absence of user keys.

However, Siebel 7.5.x versions have made deletion of data from Notes tables, using a special EIM, EIM_NOTE_DEL. The EIM_NOTE_DEL interface table should only be used to delete notes from the S_NOTE_* tables. To use it, users need to populate ROW_IDs of records to be deleted into corresponding columns in the interface table and then use DELETE EXACT to delete them.

For further details, please refer the Other Issues Relevant to Notes Migration section of the NotesDataMigrationGuide