I run into this every now and again where we run a moldflow for parts that will ultimately undergo a secondary heating operation.
It would be nice to have a module or something that allows you to use to account for what the part deflections might look like after a secondary heating operation. Maybe set the temperature for the oven/whatever and the length of time it is heated for.
Right now all we can do is say that a secondary heating operation may relax the stresses and negate the warp results we are seeing.