After sending a batch instance through the web service api, the web-service-folder is not being cleaned. This folder is not set to clean itself by default as the input and output files may be wanted for later use. Assuming that you installed the SharedFolders into the default location, the location of this folder will be C:\Ephesoft\SharedFolders\web-service-folder
This folder must be cleaned out manually in order to prevent current batch instances from being effected. It is best to not delete folders for batch instances that have not gone through to export.
You can use an application level script like the one provided here to clean the folder on a schedule. You would set the schedule in the C:\Ephesoft\Application\WEB-INF\classes\META-INF\dcma-scripting-plugin\dcma-scripting-plugin.properties file. The specific line to edit would be: dcma.applicationLevelScript.cronExpression=0 0 0/1 1/1 * ? *