ide doesn't update hex files

When building tiny applications to run in cyclone memory, the ide automatically produces the .hex files needed by Quartus. However the files are not updated after switching projects and doing a build. I have to go into the Quartus directory and manually delete the hex files to force make to recreate them. Is there a way to automate this/is it a makefile bug?

This is a Quartus question but related - when rebuilding just to incorporate fresh hex files, the smart compile does the minimum needed to do this, but then goes on to do an unnecessary timing analysis. Is there any way to turn this off?