Hi, 'Swag',
Please confirm for me what version and release date of OE you are using. You can find this information by selecting Help and About from the main menu. The release date is in parentheses to the right of the version number.
Day End removes orders that have been Completed, and Invoices and Credit Notes that have been printed from current. Have the Invoices and CNs that aren't removing been printed?
If not, you might want to access your Company Profile and turn the 'Mark printed to screen as printed' option 'on'. Then you can select to Print the various invs/cns using a 'Destination' of 'Screen' (set on the Print Window lower portion). This way you can print them without wasting paper.
Once printed, they should clear from current.
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Regards,
Softrak Tech Support