OK, so I figured out how to make my pages work again.
I added $QUERY_STRING to my SSI, i.e.
< ! - - #include virtual="/scriptname.php?parameter1=a & parameter2=b & $QUERY_STRING" - - >
(forgive the weird spacing, for some reasone the PRE tags in this forum aren't working)
So now a new parameter in the URL gets filled and replaces $QUERY_STRING. I recognized this from including PHP scripts withing PHP pages, but I never had to do this before when including PHP scripts in parsed HTML pages--not until this Apache upagrade. I hope I don't have to edit all of my pages on all of my sites now...