In the EpubSplit plugin settings (Calibre Preferences->Plugins->EpubSplit) there are settings for which columns to copy from the source to the new split books.
If Copy Comments is checked, and source comments is not empty, the comments will be copied prepended with "Split from:" (which may be translated in other languages).
If unchecked, or if source comments are empty, split book comments will be left empty.
However, I have noticed an issue with the way the "Split from:" is being prepended that causes problems with certain existing comments HTML.
If I fix that, I'll consider changing it to more closely do what you'd like.
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