It sounds like you're using the DegenGeom output.
There are a few ways to go.
The most simple would be to write a short (say six line) script in OpenVSP's built-in scripting language. You can run that from the command line to generate your files.
You would probably also want to use the DesignVar capability that makes changing parameters in an optimization setting simple.
If you want to get more sophisticated, you could compile OpenVSP with a binding to Matlab that would allow you to access OpenVSP's capabilities directly from an API via Matlab. You could use that to trigger any action - including writing out the DegenGeom files. Or, you can even access the DegenGeom information directly in memory.
Name this file degen.vspscript
void main()
{
//==== Set File Name ====//
SetComputationFileName( DEGEN_GEOM_M_TYPE, "DegenOutput.m" );
//==== Run Degen Geom ====//
ComputeDegenGeom( SET_ALL, DEGEN_GEOM_M_TYPE );
}
Then, execute it from the command line via
vsp baseline.vsp3 -des changes.des -script degen.vspscript
or
vspscript baseline.vsp3 -des changes.des -script degen.vspscript
You may want to change SET_ALL to something else.
Hope this helps,
Rob