
The only time I have ever seen 'lost', is when you EXIT with malformed files.
Look under: Misc in the File browser
Sigil flattens folders, you can NOT have 2 files with the same name, with only the Originating FOLDER name being different. The flattening process will stomp previous versions.
Code:
..\chapter1\img01.jpg
..\chapter2\img01.jpg
Only the second (chapter)image will survive
AFAIK, you can NOT
CREATE this structure from within Sigil. The issue only exists if you OPEN a book with this kind of structure