I'm afraid I don't have any good answers for your questions but if you've got a good html-based source, e.g. epub or azw3, my best advice is to keep it there. If you need to edit it then why not just use calibre's editor?
Any book using tables, images, code snippets is going to be a challenge to convert to another format and doing it in 2 stages (epub to Word to PDF) won't make it any easier. Using calibre to convert directly from epub/azw3 to pdf may be OK. Going back the other way is an exercise in masochism.
Over the last few years I've done a lot of work with Word-to-html and PDF-to-html. It has been interesting and I've learned a lot, but I'm over it now. Having got clean html out there's no way it's going back in again! Admittedly my version of Word is ancient, but introducing it into my book cleaning/editing workflow is not something I would do if I had any other choice.
Still, as a software engineer, I'm sure you're up to technical challenge
