Even when there are no formal chapters, Calibre should break an ePub file into manageable size chunks. As Stanza loads the current "chunk" each time it starts you do want those chunks to be of reasonable size and not the whole book. Have you tried looking inside the ePub file (it is basically a ZIP archive) to see if the book has in fact been broken up into chunks. You may have more control over the chunking parameters in the 0.6.x series of Calibre which is currently in beta - I have not checked.
Despite all the above, I could not understand the requirement you stated to remove the ePub formats from the Calibre library. Why not just leave them there? Calibre is quite happy to have multiple book formats simultaneously in its library.
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