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Default batch delete

I have a file of about 10,000 lines that I down load each week. this file
contains SKU numbers I have a list of about 1,000 sku numbers in another file
that have to be deleted out of that big file each week before the big file
can be used. is there a way to run a batch delete using the list of 1,000 as
a guide of the sku numbers to be deleted from the 10,000 line file?
 
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