When you run Setup.msi for either Expense or InvoiceConnect and the file Dynamics.exe.config is missing from the Dynamics GP folder, it will automatically create it.
Also, it will look at a combination of the local registry, SET file, and dlls in the folder and addIns folder to determine which AddIns to add to the file in the <addins> section. If it adds some that are not properly installed, it can cause GP to no longer start-up. In that case, comment out the ones that should not be included. See the screenshot attached for an example.