We would need a step-by-step instructions how to replicate this issue. I have tested it several times but without success.
I have performed the following 2 tests.
1.Add a few External Paths on the slave machine > Start VR spawner manually > Run DR rendering with “Restart Server on Render End” > After the job is complete I open 3DSmax Design 2015 on the slave machine and the paths were still there.
2.It is the same test basically but this time I also added different project folders for workstation and slave machine - the result was the same the external paths were preserved.