I understand that you are trying to find a way to export your model in R2016b to R2006b and potentially need to change SLX to MDL for the file extension. Despite the huge jump in number of versions, Simulink is backwards compatible and you also can save an SLX file as an MDL file. In order to save the model to the earlier version, use the "save_system" function on the model open in R2016b to save it to R2006b.
Example:
>> vdp;
>> save_system('vdp', 'vdp_2006b_version', ''ExportToVersion', 'R2006b');
And a model named "'vdp_2006b_version.mdl" that can be opened in 2006b will be saved in your current working directory as a copy of the "vdp.slx" model.
Reference to the "save_system" function in MATLAB is provided below:
https://www.mathworks.com/help/simulink/slref/save_system.html
A couple of points to note:
- The model must be open in Simulink in order to have it exported to earlier version via the "save_system" function
- You do not have to specify the extension of the new exported model as it will automatically be saved as MDL file since the exported version is R2006b
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