Not a whole lot we can do without steps to reproduce (preferably without calibre's Open With being involved). I will note that the modification time on Sigil's temp directory will have little correlation to the last time an epub might have been saved.
You're certain you weren't manually accessing the contents of Sigil's temp directory at any time during this extended edit?
I freely admit that workflows that involve the same epub being left open for weeks at a time baffle the bajeezus out of me.
