In this case congress passed a bill clearly forbidding this action, so it will likely go back to congress and Trump will have to get them to pass legislation to set aside the previous legislation in order to execute this move
(at which point members of congress will have to go on the record voting for something greatly hurting their state universities and trying to cripple scientific research which might not be so easy)
The problem will be getting the administration to abide by any count decisions against what they are doing without some kind of punitive actions against the department involved
Comments
(this one UPenn is one of the plaintiffs):
https://www.acenet.edu/Documents/AAU-ACE-APLU-Complaint-NIH-Funding.pdf
In this case congress passed a bill clearly forbidding this action, so it will likely go back to congress and Trump will have to get them to pass legislation to set aside the previous legislation in order to execute this move