I have about 4 BSS projects on the go. When I flip between them, the 'export to' path seems to get overridden in some projects. I need to check it each time to ensure I'm not replacing another site's exported site.
Sorry that you've run into problems! This can occur if these designs were created by duplicating the bsdesign in your file manager. This causes them to share an internal id, and Bootstrap Studio doesn't know which export settings correspond to the correct design.
You can remedy this by doing a Save As of your designs. This will cause the project to be saved with a different internal id. You only need to go through this once.
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I think this is important enough to be clearly stated in the documentation on the website as it can really mess some things up.