EpubMerge combines whole books, so no.
My
EpubSplit plugin can be used to 'split out' just the sections you want, leaving behind those sections. Assuming they are isolated as their own files or ToC entries
Or you could use a different epub editing tool such as calibre's Tweak Book.
(I'd recommend Sigil, but it doesn't handle EpubMerge's output well. This is a known issue with Sigil.)