What happens to the Mandamus after my I-829 was denied for my EB-5 visa?

Now that they have responded with the answers to the I-829, the mandamus is no longer applicable.

If the denial was baseless, #1 ignore it, but #2 argue it was an act of retribution.

Discuss with mandamus attorney.

Since the I-829 is denied, the government will move to dismiss the mandamus. You could challenge it and argue the I-829 adjudication is not final since you have the right to a de nova hearing in front of an immigration judge, or you could argue that the motion will be pending therefore it is not final.

The mandamus sounds academic and moot at this point since they responded. The better practice is to notify the court that the application should be withdrawn since they responded. It is another matter as to whether your pleading should be amended to cover the denial itself (i.e., a declaratory judgment).