Take a look at this SNP analysis workflow to see how you can filter for Recombinations from your VCF file. You can do it manually or with Gubbins algorithm. I could not find any downstream workflow of filtering ClonalFrameML, but the mentioned thread has programmatic ways to do the filtering. You might take a look and see if it might be of some help.

Alternatively you might also take a look at this thread.

It seems they have used ConalFrameML in both ways , either removing and not removing the recombinations. In any case if the method is not specified in the paper or in any of their blogs you can write to the authors as well to list out a filtering strategy if they have which can be shared.