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GeoRaptor's loader is a create table/insert loader. It currently does not enable the appending of shapefiles to an existing table.
If you have a bunch of existing shapefiles that can be loaded in one go, then that is what the GeoRaptor loader will do.
Some ideas exist in the code for an append mode, but these ideas remain ideas.
If you want an append mode please make a feature request at out source forge account.
Even better, if you want an append mode, make a donation towards it.