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pragma integrity_check; Error: disk I/O error
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> So whether the culprit was some system bug, AV bug or just memory crap piled up is not clear, but the AV interference sound a sensible option. Wonder if the lib/tool can be made more robust on that.

AV interference is not an uncommon problem on Windows. Libraries like sqlite have *zero insight* into what such a tool is doing and how it may be interfering. The "real" (if snarky) answer is to make the OS more robust so that it doesn't need AV running 24/7 ;).