Hello,
Indeed, all the segments of recordings identified with an event that includes the tag “bad” will be ignored from the ICA analysis. The problem with removing blocks of recordings is that you create discontinuities in the data, that might lead to specific ICA components to explain the jumps. I think there is the same issue with epoched data, but maybe I’m wrong…
I am not familiar with the epoched approach of ICA (or with ICA in general…), follow the EEGLAB recommendations if you can. When I wrote this process, I was recommended to use continuous recordings rather than epoched ones.
This process is calling directly the EEGLAB function runica. You should be able to call this function in a similar way as what you were doing in EEGLAB, and hopefully obtain similar results.
Francois