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The variables point to paths defined in the make file (subscriber.mk) Can you look at the make file to verify that these lines are included?
$(NAME)_RESOURCES := apps/aws_iot/rootca.cer \
You can modify the certificates in the directory pointed to by the make file ( by default it should be C:\Users\username\Documents\WICED\WICED-SDK-3.5.2\WICED-SDK\resources\apps\aws_iot ), or modify the make file to point to the path that your certificates are in.