We currently do this same process to create our i-Models on a nightly basis. You will need to create a dgn file that has the models that you wish to publish as i-models referenced. Create a batch file that opens the file and by using the -S command line option you can call a text file that publishes the models using the "Publishdgn" option described above. We found that about 50 models per file, any more that that and we get memory errors.
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