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The only thing I can think of is that the Mac OS only removes files/folders from temp that have not be accessed (read or written) to in 48 hours. Upon import if an epub is opened its META-INF and container.xml will only be read once and then never checked again. Whereas the text files that are edited/read and any resources they reference are always being accessed. If you wait a long time without saving, the meta-inf and container.xml may actually get deleted out from under Sigil, whereas the more recently accessed text and resources would still be alright.
So if Sigil recreates a missing META-INF and container.xml upon first load of the damaged epub, but you do some editing and wait long enough without saving (48hours) you might end up with missing pieces. The key is when no saving is done while leaving the app running longer than 48 hours on a Mac, you may run into problems caused by the OS and not Sigil. Sigil can prevent that issue if you give it a safe temp location to use.
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