Have Novus Ordo bishops, disregarding Summorum Ponitificuм and Universæ Ecclesiæ, ever kicked out indult groups like the FSSP and ICRSS from their dioceses?

I haven't seen any evidence of that where I live. 

Yes, definitely.  I’m not talking about those with large, well-established separate buildings, but those sharing novus ordo facilities.  They don’t necessarily kick them out in dramatic fashion. Instead, they’re slowly marginalized to the point where it can be said there is no longer enough parishioner demand and shut them down without fanfare.  I know of two diocese where this was/is currently under way.  The COVID thing makes it particularly easy to just have the extraordinary form never return. I won’t be at all surprised if many novus ordo churches never return and entire parishes, even diocese close their doors for good. Has there been any reinstatement of mass requirements from the bishops?  If mass remains optional for all, then look for the already shrunken number of practicing Catholics to shrink even further.  
In my mind, however, this may be a good thing as it will sift those with faith from the majority without.
For many, semi-regular mass attendance was the only thing separating them from those who gave up all religious observances. In a post-COVID world, one will need to go out of his way to find a mass, a sacrifice most will not bother to make.  

Have you ever seen indults simply leave a diocese, on what seems like their own accord?

No, I haven't. But where I live they appear to be very integrated into the archdiocese. They have a full program of catechesis for the children. And a few years ago they hosted a diocesan event with the Legion of Mary.    

No, I haven't. But where I live they appear to be very integrated into the archdiocese. They have a full program of catechesis for the children. And a few years ago they hosted a diocesan event with the Legion of Mary.    

The SSPX is, too.  A few years ago, maybe 10, Fr. Kenneth Novak of the SSPX organized and encouraged the SSPX chapels in the area to participate in a Fraternity of St. Peter and diocesan-led event.   Also, one of the SSPX chapels in the area has a coordinator who is high up in the local diocesan Knights of Columbus.  Seems like a conflict to me, unless he is a plant to destroy that chapel.

"Leftist Italian bishop stamps out traditionalist priestly fraternity" (Feb. 2020)

That was notably harsh as their priesthood was suspended. This is at the level of penalty for abuse of children. Francis reversed many defrocking of abusive priests, including abortively one Inzoli whose dismissal was only upheld when he was sent to prison. Francis helps bishop's conferences, like the Italian bishops to vent their hatred against the Catholic Mass.  If they have no corporate outlook, he does nothing.

Not in Minneapolis. The Fraternity there is vibrant and well attended, from what I hear. If Hebda (the head of the archdiocese) even tried, they'd burn his office down.

Which is why I refer to Pope Francis as a friend to Catholic Tradition. He helped the SSPX with their immigration problems in Argentina when he was Mgr Bergoglio. (I believe that would be Mgr Williams)