`MDNode::replaceOperandWith()` changes all instances of metadata. Stop
using it when linking module flags, since (due to uniquing) the flag
values could be used by other metadata.
Instead, use new API `NamedMDNode::setOperand()` to update the reference
directly.
git-svn-id: https://llvm.org/svn/llvm-project/llvm/trunk@225397 91177308-0d34-0410-b5e6-96231b3b80d8
