Smart compilation disabled by automatic script execution?

Interesting. It definitely seems like incorrect behavior, and you might want to file an SR.

If you want a "Not-so-smart" recompilation, go to Assignments -> Design Partitions. If you're not using partitions, one still exists called Top, which is essentially your top-level. Just change the netlist type to Post-Synthesis, and it will skip synthesis, or post-fit to skip the fitter. Actually, since it's user controlled, it actually is Smart, but you have to remember to change it back. Not ideal, but might save some time.