Is there any way to re-analyze your data with a different cluster cutoff point (say 0.4 instead of 0.6 for FCC) without re-running the entire process?
Yes - download the full archive of the run and perform a manual analysis
See: https://www.bonvinlab.org/software/haddock2.4/analysis/#manual-post-docking-analysis
In principle all required scripts are in the tools directory in case you don’t have a local installation of HADDOCK