LES presence/absence/operation is irrelevant. If your main engine is not conducting burns as commanded, then the first thing to do is to figure out why it did that and rule out that it cannot happen in other stages of flight. This could be something unique to disposal burns, or it could be an issue that could occur at any time but just happened to luckily crop up in a disposal burn this time. If it's the former, then RTF can be as rapid as with the last two F9 standdowns. If it's the latter then the issue needs to be resolved before RTF which will take longer.
SpaceX pauses Falcon 9 launches after rocket second-stage anomaly