The Kron feature under Cisco IOS and Cisco IOS XE has multiple known bugs. Recently it showed , that a Ciscio 3850 running IOS XE 03.03.03SE with a configured Kron job for auto backup lost parts of it’s running configuration.
After the Kron job was executed, parts of the Kron configuration itself and also parts of interface configurations were missing. Mainly the execution time configuration of the Kron job got lost but also special port configurations of uplink ports, which made the bug critical.
We now use EEM scripts as alternative solution to the Kron feature. See http://www.cisco.com/c/en/us/products/ios-nx-os-software/ios-embedded-event-manager-eem/index.html for more information.