If an inactive taxa remains for some reason on a checklist (not really sure why it should, but clearly it happens), then it should be excluded from the output of using the compare tool.
For example
https://www.inaturalist.org/lists/51966-Wellington-Check-List/compare?page=4&utf8=✓&with=7219
As I write, the 2nd and 3rd species on the right list are inactive, they should not be in the returned data.