I didn't create this ePubs, but found it as it is, from "various" sources (I am an archivist)
It was really very rare and it was especially me who was not lucky to have encountered such a problem.
As it is precisely rare, random, difficult to perceive and on existing files, it is for me unthinkable to have to check all the books.
The problem is not to fix the <manifest> but to know that it must be fixed (I agree that KevinH's method works).
What if I save the ePub without knowing that there were non-indexed files....

byebye, the files are losts.
I have launched a "Modify ePub" on my entire library, and I would launch a "Quality Check" tonight, but the risk will always be present for the new books that I will import and open in the stride.
I agree that given the design and operation of Sigil:
1) It is difficult to qualify his normal bug behaviour.
2) That you are a volunteer on the development of Sigil.
3) That there are other much more useful feature to implemented.
4) That apart from this very specific and rare problem, I have never encountered a bug (ah, once, 9.12: INI + UTF-8

)
For me, the subject is closed.
Thank you for answering my problem. Even if it won't be solved, at least I understand the why, and that some avenues of help were given, so I could act accordingly.