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Where are the SharePoint files sitting? Have you created a sync? One thing you can try is setting the run as setting to run workflows as yourself. If you are using a server to schedule to, try to check to see if the sync is created on the server.
Please note: SP files as input data are not an officially supported data source (SP list inputs are supported), however we have seen some customers use them when scheduled without issue. Generally, there can be access or permissions issues with the service account.