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A straight forward approach would be to just run two standard data points each with their own OSW, a baseline and an improved (or at least altered in some way). If you really want to do it In a single OSW, you can create a custom OpenStudio model measure that takes a copy of the seed model and runs a simulation and reporting measure. This would be done by running an OSW within the measure “Inception Style” This isn’t that crazy, it is how we do sizing runs in measures, but it does seem like a complex solution where there may be a more direct approach. After this measure the rest of the “improved” workflow would run and then the reporting measure. You would have two full annual simulations and two HTML files.
An alternate approach is to run a more typical workflow for the model and energy plus measures but put in a special reporting measure. This reporting measure would contain run an OSW on a copy of the seed model, which you should have access to, without any extra measures and runs the simulation. Then you can generate an HTML file that uses SQL results from both the seed simulation and the improved simulation.
To step back a bit, what is the reason that you need to run the measure twice in a single workflow. That might help to determine if it really is necessary to run it in a single workflow and what the solution might look like.