Atlantis Word Processor simulates "small caps" formatting in the eBooks it creates by applying both the uppercase pattern and a reduced font size to lowercase letters formatted with "small caps". In other words, instead of keeping the "small caps" formatting of the original text, Atlantis converts it to uppercase with reduced font size. It won't be "small caps" per se but it will look exactly like it in any eReader. You can find details in the following blog post:
If you converted your eBook to the RTF, DOC, DOCX, or ODT format, then loaded it to Atlantis Word Processor, you would have a simple workaround for the problem with small caps.