When running 4D Server as a Service and updating the strructure file, it is usually better if the structure file is compiled and has the "Use new architecture for application deployments" compatibility option enabled. This allows the location of the last used data file to be stored in an XML file stored within the users profile folder of the OS.
Otherwise the location of the last used Data File is stored within the 4DB structure file and it could be referencing a different location than what you may expect. Therefore, it is important to verify that the location of the data file is correct by launching the application on the destination machine first as a standard application prior to running it as a service. This extra step will allow the devloper or administrator to confirm the correct data file is being used prior to launching the service.
Ultimately, the preferred solution is to use a compiled application along with the Use New Architecture option.