I cannot replicate this. Steps I tried:
1) Right click a book and select edit book
2) Click File->Add a new file
3) Chose the name as itunesmetadata.plist
4) Enter some dummy content into the file
5) Click save and then quit
5) Click save to disk
7) Open the saved epub in the editor
8) The itunesmetadata.plist file is stil present
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