As you want a incremental load of the data you cannot use the "Load and Deactivate" import event operation. You can use two separate events first use Load operation for Plant.csv and use Deactivate operation for Plant_delete.csv. From the error you have metioned looks like the batch program is unable to find the Plant_delete.csv file. Please ensure you are placing the Plant_delete.csv at the correct path and under correct partition. Say you have part1 as partition under variant var1 then the import event by default will look up for the file under Server/config/variants/var1/partitions/part1/data folder. Also ensure the file properties are correctly set.
Thank you for your reply - my question was probably not clear enough.
However I have soreted the issue- the error given when loading using Batch upload was caused by the name of the file - I used Plant_Delete.csv instead of Plant_delete.csv and all works fine, the deactivated plants are deleted from the Ariba data.