I have seen something like this happen because a network interface card or connection was bad. The workstation was able to enter and post, followed immediately by printing, but the invoice was not written to the network files and later could not be found. In that case it was not in the day end and not in the Customer transactions.
Make sure opportunistic locking is off. You can use chksys.exe in the Softrak\system folder to verify this.
Are all users using the same program on the network drive? Having more than one set of program files could allow one workstation to overwrite the changes of another one because file locking is not able to work properly.
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Kate Spontak
Stief Group
New Jersey, the Garden State