[DiapDealer]

There should be no damage to your clips by opening files in parallel with Sigil. That's never been my experience after years and years of Sigil use (both old and new). Something else has to be going on there. Many people (myself included) have multiple instance of Sigil running without any issues like this.

As to your number one issue, the allowed metadata (including syntax) in Epub3 has changed drastically from Epub2. I have no idea what custom tags you're using with calibre, but I doubt very highly that they're a part of the epub's internal opf. It's more likely they're used in the external metadata opf that Calibre creates for each book.

All of your other mentioned issues sound to me like they can be attributed to either a corrupt Sigil ini file, or possibly two different installations of Sigil trying to share the same preferences.

You certainly shouldn't be having the troubles your having with the latest Sigil. It's not been the experience for the vast majority of users out there.