You ran "qmake -project" which generates a template PRO file listing all the headers and sources in the directory. That is, you asked qmake to overwrite the existing pro file with a template. You never need to run this more than once when first setting up your project (it's not essential then either).

If you modify Q_OBJECT macros in your headers, or add/remove sources etc. then you should run "qmake". This rewrites the Makefile based on the rules in the PRO file: it does not modify the PRO file.