Smart compilation disabled by automatic script execution?

A final thought... You have some way the user "chooses" which VHDL file to use, whether it be a configuration statemet, or you're just adding/removing a different file. Maybe you could use revisions, whereby one revision adds file A and writes out a .sof called fileA.sof(or whatever name makes sense) and another revision for file B. The revision is listed at the top of the Quartus II project, so the user is less likely to be confused, and since they're already doing something to switch what file is used, that might be a good solution.