No, don't delete the whole file! The system is not really designed to have PLUs deleted, you just put your new products over the old ones. I think there is a way to inhibit a PLU if you don't want anyone to use it. The difference is with scanning PLUs. I am assuming you are not using a scanner. Are you using PLUs on the keyboard only?
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If anyone needs more information, the Sam4s / Samsung ER-650 manual is here:
http://the-checkout-tech.com/manuals/cashregisters/Samsung_ER-650_and_ER-650R_operating_programming_manual.html
Registerman
August 2012