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The note would have been uploaded to the servers, and can be searched using the web platform.
You can review the activity log to see activity with the note.
I've got over 13k notes, and not noticed a problem with notes disappearing.
Accidental deletion is possible, but the note is moved to the Trash and can easily be recovered
I have confidence in Evernote, but I maintain data backups; I have a recovery option if necessary
>>if it is related to checklists
Checkbox is simply one element in a note; I doubt it has any significance.