You can click and drag the projects in your project list or inside a portfolio to control how they show on the website.
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Homepage order is initially controlled from the main projects list; however if you have a homepage portfolio setup to control the selection of projects on the homepage then you will need to change the order of the projects inside that portfolio.
You can check if you are using a portfolio for your homepage in Settings > Homepage Section > Homepage projects/portfolios source.
Examples:
'All projects' means it will use the main projects list from my work section as the feed and thats where you will control the order.
Portfolio name means its using that portfolio so you will control the order of projects inside that portfolio