[FuncSpec] Invalidate analysis by setting MadeChanges explicitly (#155833)
As reported in
https://github.com/llvm/llvm-project/issues/154668#issuecomment-3233294078,
we missed invalidating analysis as we don't set the MadeChanges to true
after removing dead functions.
This patch makes it explicit to remove the dead functions marked by
FuncSpec in SCCP and set MadeChanges correctly.