The convert_gen2_repo_to_gen3 script has been replaced with a butler subcommand called convert. Help about how to use the new command can be found by running butler convert --help. It is very similar to the removed script.
A note about the environment butler runs in: the butler command is defined in daf_butler, and convert is loaded dynamically from obs_base; make sure you have setup these packages before calling butler convert --help or using butler convert.