Supposedly, if you do
setenv AFNI_RESCAN_AT_SWITCH NO
then run AFNI, you'll get the Rescan button back. The reason it disappeared is that the default is now to rescan the current session when you press the 'Underlay' or 'Overlay' button, so that a manual rescan is less needed.
However, there's a bug in AFNI so that this setting NO didn't make the button re-appear, as it should. I've fixed that, and will probably recompile new binaries early next week.