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I have not been saving the .qdf file like Brad suggested, but I am going to look into it--maybe I have been missing something.
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See the comments at the top of the .qsf file for some information about the .qdf file(s).
The Quartus Default Settings File, or .qdf, is required if you are using a setting value in a .qdf in the project directory that is different from the setting value in the .qdf in the Quartus installation directory.
Most setting value defaults do not change from one Quartus version to the next, but there are sometimes changes. The .qdf file allows you to change Quartus versions without a change to the values of settings that are not given explicitly in the .qsf file. If you have a .qdf file that has the same contents as the one installed with the currently used version of Quartus and if you won't be changing the Quartus version, then the .qdf file does not matter.
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