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@mmiso, based on your last comment, it sounds like you may have an EnergyPlus error, which I admit is represented a bit oddly in PAT. The screenshot below shows a design alternative with a status of "completed Fail", but there are no errors shown. In this case that is because the warnings and Errors for the EnergyPlus run don't bubble up to the summary row for the design alternative.
To view EnergyPlus Errors and Warnings for a design alternative just click on "EnergyPlus Results" and scroll down past the warnings. As a note, this is also how you view warnings and errors and other messages on individual measures.
You may consider re-naming to something like "Simulation didn't finish but no errors shown" instead of the saveAs. The saveAs I think is un-related to why your simulations are failing. Not sure why the server wasn't starting for you before you removed the extra file, next time add additional seeds via the GUI, it could have been an issue with an unexpected file.