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I have a project that uses multiple DEM tiles to create a Virtual Raster Layer. The Virtual Raster is then used to calculate a Slope and an Aspect layer.

I've attempted to save the Project, but when I open the Project, the virtual and subsequent layers are not found.

How do I save the Virtual Raster with the project?

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I think you do save the project but what you need to save first is the VRT file generated by "Build Virtual Raster" (illustrated below). Then, when you will reopen the project, you will not "lose" the VRT.

Build Virtual Raster menu for file saving

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Make sure the layers in your project aren't temporary in-memory only layers. If so, as soon as you close QGIS, they are wiped. The layers will appear in the layers list in your saved project, but the data will be absent.

In-memory layers are indicaed by a chip symbol on the right of the layer:

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There is no way around this, you need to save the process resulting layers to disk if you want to keep them. From the right-click dialog menu in the layers list, either use Make Permanent or Export -> Save Features As...

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