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I can not recreate this crash either. So we need more details in order to track this down.
Specifically, how *exactly* are you changing the bookid ... what to what. Is the bookid a dc:identifier that has a uuid scheme? Are you using IDPF or Adobe? How exactly are you saving the file after the change to the bookid? Is it a "Save", "Save-As" or via an output plugin.
Please note that deobfuscation always happens on load (assuming the right xml exists) and any obfuscation if enabled, only happens on Save of the epub to the version in the file. Not the fersion stored in Sigil's working directory.
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