Rather than removing and appending, replace the "action" argument with -fsyntax-only to preserve its relative location. There are some flags for which Clang will interpret a subsequent argument which doesn't start with - as an argument to that flag rather than a standalone argument (such as the source file). While removing any argument runs the risk of causing this problem, the source file path generally follows the action argument so we can mitigate this problem by preserving its location when replacing it with -fsyntax-only.

It's likely we want to use a smarter mechanism such that when we remove a single - argument, if the subsequent argument does not start with - it gets moved to the end or something, this should improve the situation for now.