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There are actually two circumstances when %Include directives are executed:
At compile time. As a consequence, the compiled agent code does contain any code that was inserted via %Include directives. The included source code files are not needed to execute the agent code.
When an agent is executed under debugger control. LotusScript then tries to access the source code contained in any included files in order to present that source code in the debugger. An error occurs in case an included file is not present at the time when the relevant agent is executed in the debugger.
It seems that the documentation correctly reflects the first part, while the second part is missing.