The old Sigil would automatically force a restructuring of the file system to keep everything in a standard location. There were some reasons why you might want to keep it the way it was originally put together…. So, the Sigil default now is to leave the file structure as it is.
You can, however, make it go to the Sigil standard by clicking on the tools menu and then “restructure epub to Sigil norm”.
Quote:
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Restructure Epub to Sigil Norm: Starting with Sigil 1.0.0, EPUBs loaded into Sigil are kept “as-is”; no files or folders are moved or renamed. This is a departure from Sigil 0.9.18 and earlier, which automatically restructured each EPUB into a standard Sigil form (one OEBPS folder, specific names for the OPF and NCX, only one folder for text, images, etc.). Users who prefer the standard Sigil form may use Restructure Epub to Sigil Norm to manually restructure their EPUB to the old Sigil standard.
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I almost always do this… and then you can use the “../Fonts”… otherwise you need to use the actual path to the files. You can see that path if you hover over the file in question, or go to preferences and select to always see the full path.