If these eBooks have no DRM or have had the DRM removed, use Calibre's editor. Start with removing extra CSS entries. That helps alot given how many extra CSS entries are used because a lot of publisher (from the BPH) use a catch-all CSS.
After that, it's very easy to go into the CSS, find the offending code and fix it. I do this because I do not like paragraph spaces.
As for Kobo, there is no way to override these paragraph spaces other than editing the CSS.
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