You haven't lost any project files, just the project list in project manager so no need to worry. It is healthy to close projects you are no longer working on and free the project manager. In earlier versions of the program the more projects you had in the project manager window meant a longer startup of AcadE. Each time I install fresh and clean my project manager reverts to only displaying the default projects that come with the program for learning. What you are describing is a normal situation. Just click to Open a project and navigate to the .WDP file for the project(s) that you wish to have readily available in project manager.
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