The application folder often contains a number of different builds (for Simulator and actual devices) and sometimes repository data, so you should not have to worry about the size difference. The folder of one of my iOS projects has a size of 25MB, while the IPA only has 6 MB.
Moreover, PNGs are optimized for iOS while compiling, so if the original PNGs were not much bigger before, an image size of 4KB does not necessarily mean something is wrong.
I'd suggest you to concentrate on the real problem, which must be related to your provisioning profile. Have you made sure that your provisioning profile includes the device you want to install your app on?