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Sorry this is coming late (and I might have helped you with this particular issue Amir - I can't recall), but I can further the answer here for others looking in the future.

You can definitely do things in the Wizard stage which will not show until you try to simulate. Notably, there are many possible issues with regard to geometries and window placement.

If you can navigate back to Wizard and re-generate the INP by clicking "Finish", it's a good sign that you haven't lost any work. My first inclination in such a case is to "Finish" wizards, save, close eQuest, and reopen the project with mind to see if any BDL cautions/warnings/errors pop up. If so, close the project, open that BDL file, and navigate to such messages to get a sense of what might be awry... you'll often get enough by context to know what needs to be fixed in the wizards. You can also try at this stage (if you're ready to push on to detailed edits) to directly edit the INP prior to re-opening to resolve the BDL messages.

Hope that helps someone in the future!