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Again, since an epub is a zip file. Unzip the problem epub outside of Sigil. Then open a copy of the epub in Sigil. Navigate to Files->Add->Existing Files... and add any missing files (xhtml, images, fonts, styles) you feel are important but missing in the manifest by visually comparison to the unzipped version.
If you are afraid you might have a problem epub but are unsure, simply run epubcheck on it, which will happily report there are files that are unmanifested.
This can all be done right now with no changes to Sigil.
If this problem is so very common for you, then create a plugin that can parse the opf and compare it against the files provided in the epub/zip and do what you want.
This is not really that hard. If you do not know python, think of it as an excuse to learn or ask for help here.
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