Update. The invalid connections come from the following references inside the package.
The package after being deployed, still works inside Visual Studio and from SQL Server. My guesstimate is that Visual Studio checks if there is a connection manager with that GUID and then uses it. Shouldn't the package importer also do this?
I receive the following errors when importing a SSIS project into BimlStudio. Please contact me through slack to receive the project files.
Connection invalid. Only GUID shown.