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Originally Posted by DiapDealer
Not a whole lot we can do without steps to reproduce (preferably without calibre's Open With being involved).
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Yeah, I knew that. I realise "leave Sigil open for ages" isn't really a step. Really at this stage I'm just reporting what I've seen since it's happened twice.
After I reboot to do the Win10 patching, I'll start Sigil from Cygwin so I can capture any console output (if any).
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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.
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I meant that was likely the time that the images and cover and container.xml disappeared, since adding or removing a file will update the directory timestamp.
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You're certain you weren't manually accessing the contents of Sigil's temp directory at any time during this extended edit?
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Yep, absolutely certain. I had to go hunting to check what was inside that dir.
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I freely admit that workflows that involve the same epub being left open for weeks at a time baffle the bajeezus out of me. 
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This is a "tidy up a bit when I feel like it" exercise. Hence no changes for almost a week. No rush
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Originally Posted by Doitsu
Since you're apparently working on a Public Domain book, can you please also attach the actual epub?
This'll make it easier for KevinH and DiapDealer to narrow down the issue.
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I've attached it here (the previous version that still had the images), although as pointed out above it's not likely to help narrow down the issue.
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AFAIK, macOS Sigil users occasionally lost files, if they kept epubs open too long in Sigil. If you're a macOS user, you might want to change the temp folder location (Edit > Preferences > General Settings > Advanced) to a non-system folder.
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Win10 (mentioned in first post).