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Makefile from qmake should have 'make clean' option that removed all .o etc files. Then try to run make again. If it doesn't help check your time settings. See if your time is correct and if edit time of the modified files is correct.
Make checks timestamps on source files and .o ones. So if you don't want to run the autogen script again (what may be hard if you add new files) edit them, then make should consider them as modified and compile.
If you want to make to think the files have changed without actually opening them up in an editor and messing with them, just use touch. It will change the modification time to the current time. So if it's a bunch of c files,
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