I’ve ran into this problem at several clients, and this latest was the result of removing a few items from the Global Navigation.  The issue being that after we made changes to the Global Navigation, all Project Sites suddenly showed up at the bottom of the left navigation of Project Web App.  The steps below corrected this issue:

 

Step 1) From Project Web App, Navigate Site Actions –> Site Settings

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Step 2) Under Look and Feel, Select Tree View.

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Step 3) Uncheck Enable Tree View, then click OK.

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Step 4) This change may take a few minutes to propagate. It may even require logging out/in to Project Web App. Ultimately after a few minutes you should no longer see the subsites in the left navigation of Project Web App