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And drag and drop only impacts the order of the spine not location. Remember the BookBrowser shows files organized by file type (ie a virtual folder) not an actual folder. You can use the right button pop up menu to Move where a file is actually stored inside the epub.
It helps to use Sigil preferences to set it to show the full book path of each file.
If all fie names are unique, the easiest soluation may be to use the Tools->Restructure To Sigil Norm menu to have it move everything into a nice normalized structure in one go. It will automatically update the links to match.
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