When you delete files/contents from the project bar, they're not actually deleted in the .capx. The file size stays the same.
1. Make a new project
2. Import a file (I suggest a music file to see .capx size difference)
3. Save the project file.
4. Delete the file/music from the project bar
5. Save as a new project file
6. Observe how the 2 .capx files are exactly the same size despite the 2nd file not having the large music file.
At the moment this means you should never import something into your game unless it's finished quality (i.e., this will never be the case though as games take a lot of iteration) if you want to keep your .capx file size low.