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Yes, you can use vendor and MSC in the same firmware.
For this, you have to define one of the interfaces as mass storage (Refer to the descriptor file in the FX3SMassStorage example that comes with the FX3 SDK) and an other interface as Vendor (Refer to USBBulkLoopAuto example that comes with the FX3 SDK). Also, the USB endpoints have to be configured to handle mass storage data and the vendor data.
We do not have a ready example that implements both but the endpoint configuration and the descriptor from these two examples can be merged to generate a firmware that has both the capabilities.