Frank Cotroni wasn't even a force in his later years, especially after his last release from prison. I also wouldn't jump to conclusions and assume the Cotroni group has all of a sudden regrouped, and become a force within the Montreal Mafia like old times. If there is some newly consolidated Cotroni group, I'd place it in the same group as the typical factions. Meaning it's group comprised of other Italian Canadian & French Canadian criminals moreso than Cotronis themselves. In other words, I simply don't believe there is anything at this point to go on that leads to them suddenly being a standalone faction.
Despite the power shift, Frank Cotroni appeared to maintain considerable influence in Montreal's underworld. In July 2002, he was still described in police intelligence reports as "an important person in the Montreal Italian Mafia and in Canada."
In '00 period before he died in '04, which are the "later years" I'm referring to, Cotroni wasn't much of a factor in the Montreal underworld, this is at least according to The Northern Connection & Peter Edwards. Not saying it's facts, but there's no reason to assume Edwards wouldn't have an idea. A law enforcement officer from the time is quoted as saying "he's slowed down quite a bit. The organization is in tatters, if you want to call it an organization." This officer is unnamed however, and I don't know which organization he's referring to, most likely the Cotroni group itself, meaning the direct group whom was under Cotroni & his brother themselves. He definitely stayed in contact with various undesirables though, I won't deny that, which was his reason for going back to prison in '02 on a parole violation, meeting with a man who went on to meet with old Cotroni associates. I believe he even released a cookbook during this period, I wonder how guys would've felt about that. It's not exactly writing a memoir but who knows.
Chapter 28 of the aforementioned book details the murder of Franks son Paul in '98. There's another quote by another unnamed member of law enforcement, granted, but the rumors were to them that the killers did a sort of risk assessment before they killed the kid and they supposedly determined "They (Frank's Crime Family?) didn't have the clout in place..."; Meaning the "old Cotroni group" of Frank's didn't have the clout to avenge the death of his own son. These were supposedly bikers, as rumors were he was selling diluted cocaine to biker gangs. Again, rumors, but again Edwards was also a reporter for these groups specifically, and this specific book is usually referenced when sometimes the Cotroni's come up in other places. But hey, he could be wrong, I don't suspect him to be right about everything.
As far as the current status of the immediate group, I think Frank's son Francesco is still around, he served time for murder before, and if he isn't in prison I can see him being the representation for the "Cotroni group", I guess in the same way Leonardo would be for the "Rizzuto group", so I could be wrong about they're current place within the Montreal milieu.
The risk assessment turn out to be wrong, the person that ordered the killing of Paul Cotroni, Johnny Plescio one of the founders of the Rock Machine was killed about two weeks later and his brother Tony Plescio was killed one year later. Johnny Plescio didn't like the fact the Paul& Frank Cotroni Jr. were doing business with HA.
Is there definitive proof that Plescio was killed by members of the Cotroni group though? I don't believe so. As you mentioned, they were already in a long standing war against the Hells Angels. The risk assessment simply could've been correct and someone outside of the Cotroni's killed Plescio over drugs, but unrelated to the Paolo Cotroni Jr. murder.
And we see how the Montreal Mafias game with the HAs turned out. They actually ended up empowering them and the HAs have outlasted the mafia group of Montreal for the most part. And I dont doubt the goal was to work with both groups, as evidence shows. Evidence also shows the relationship between The Rock Machine & The Montreal Mafia may have eroded over time. As Leonardo Rizzuto was involved in a fight with a member of Rock Machine, I believe this member was killed afterwards but I could be wrong. And it was I think Paolo Gervasi's kid whom was murdered by mafia loyalists for dealing drugs with the Rock Machine after HA complained. Or I may have that in reverse. And Cazzetta eventually joins up with HAs as well. And he seems to be, at least after Vito's death, the primary liason between the Montreal Mafia & The Hells Angels, him and Greg Wooley.