Jeff,
I'm not sure I fully understand your question. An m-file is simply a text file. LabVIEW can dynamically create and save these files by simply sending a string to the "Write to Text File" VI.
Now, if you are asking about calling these newly-created files through MathScript within a built application, this is not possible. In order to call m-files at all from within a built application, the m-files must be added to the project tree. Also, in the build specifications, the "Enable MathScript support" item must be checked in the Advanced settings. When the application is built, the m-files will be compiled and it is this version of the m-file that will be run with the built app even though the m-file may change in the future. The issue is that the MathScript compiler is not available in the run-time engine, so it is not possible to call m-files that aren't specified at build time.
Grant M.
Staff Software Engineer | LabVIEW Math & Signal Processing | National Instruments