[CallGraph] Update callback call sites in RefreshCallGraph

Since D82572, we keep "reference" edges for callback call sites. While
not strictly necessary they can improve the traversal order. However, we
did not update them properly in case a pass removed the callback call
site which caused a verification error (PR46687). With this patch we
update these reference edges properly during the invocation of
`CallGraphSCCPass::RefreshCallGraph` in non-checking mode.

Reviewed By: sdmitriev

Differential Revision: https://reviews.llvm.org/D83718