CK will back up as often as you want. Under CK -> File-> preferences ->Misc. You get to set whether to save or not and how often you want to save. If further clarification is needed, would be glad to upload a screenshot of the open CK prefs window.
So does this program save the unsaved edits made in the CK every interval or does it retrieve the last saved version? Currently I already backup my esp's every time when I've saved my changes, which doesn't help when my CK crashes after 4 hours without saving. If it also takes the unsaved changes made without re-creating the entire esp (which freezes the CK for a few minutes) then this sounds like a great program to have as modder.
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So basically save often if you want every edit to be backed up.