EPUB on 12.3 on MAC sfm and non-sfm books

We have the Bible books in SFM format as is standard in SAB, but Front and Back Matter books as HTML files stemming from export from DOC (which we use to import into Indesign for the printing side).
However HTML based books are not dealt with in the Pub export (they become a mess), so my question is, would there be a way to mark which books we want to include in the EPub file generation / or otherwise which ones should be omitted.
We think one Epub file with the all Biblebooks alone would be great.