Hi Daniel,
From SAP Web IDE perspective your repository is a single project (even though you put more than one application in it).
Therefore you should have also a neo-app.json file in the root level of your project (for design-time purpose only) that will include all the routes you use in all the sub-applications of this project.
The paths in this neo-app.json file must be also adjusted according to the new structure.
So, for example, if you had a route to the SAPUI5 resources with the path "/webapp/resources" you'll now have to adjust it according to the new Component.js file location, e.g.: "/app1/webapp/reources" (assuming app1 is the folder with the app directly under your project root). And you'll have to create such route for all of your sub-applications.
Also, in order to be sure you are running the application you intended to - I recommend you to select in your workspace specifically the Component.js file of the desired sub-application, and right-click on it to perform the Run operation (as the Fiori Sandbox is actually using the Component.js file as an entry point to run the application code).
Thanks,
Rotem