Currently I have purchase orders locked once they are approved and if the user is not an administrator.
This is preventing me from running Manage Intercompany Sales Orders on the PO because the system is trying to access the document and not an administrator.

Is there a way to work around this?
.
NetSuite considers “System” a User with ID -4 (sometimes -5).
If you want to enter a condition in a Workflow for a “System” user, you can do that via:

-4 is the internal id of -System-. Which means if {user.id] !=-4 is added to the condition of the workflow, it should allow the System to skip the Lock record action.