Yes, linking the two systems in Workbench and solving them in Mechanical is indeed the way I am used to work. My issue is that, when working with larger models, the generated files (model, temporary, results) can become quite large and unfortunately my PC sometimes is not able to deal with that. And as my company has a HPC cluster, I would like to use it. It has virtually no storage limitation and much higher computing capabilities.
So just to make sure, the only way to get one input file with multiple solves is via full APDL scripting? There is no way of preparing the models in mechanical using its GUI and simply generate an common input file? I saw this System Coupling system in Workbench. Isn't it possible to use it to get to what I need?