Where is this 'bring it back into calibre' step coming from?
I would expect the only steps would be:
- Import EPUBs into Calibre
- Change title of each book in Calibre
- EpubMerge the books in Calibre
- New Merged book exists in Calibre. The end.
Remember it's also an option to edit the merged book after the fact and change the Table of Contents however you would like. Calibre's Edit Book as a good ToC editing tool.