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Are you using actual "List" settings in the paragraph style or just indents. I never use "list", simply regular body text and all the desired indents and spacings. I add the list prefix letters/numbers/roman/bullets, if needed, manually as the auto list HTML can fail on some ereaders.
So all my paragraph styles are text, except any that should be in a TOC, they get a heading level. The lists look like lists and I have no indent errors.
Also I use pt for docs to be an epub, but change the editor to use cm when editing a doc to be exported as a PDF. I can save the version for epub with a new name, then overwrite the styles with a template import, add headers, footers, page numbers and change some pages to be front matter, contents, chapter start, end matter, appendix etc.
For the editing for epub conversion I use a small page size with small margins (both of which are ignored by conversion to epub) to have an idea of issues with images, lists, special styles etc.
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