Email conversation threads are getting broken during the transition to the new helpdesk

Today is the first full day of use out of our new helpdesk and, so far, the feedback has been almost all positive.  One thing that we are noticing that we did not consider earlier though is that the email conversations / threads are getting / broken between replies that were sent to the old helpdesk and replies that are being sent to the new helpdesk.  This should be an isolated issue that will go away once all of the tickets on the old helpdesk are closed out (we expect less than 30 days) but it is causing some confusion in the interim.  We’re working now to see if there is a good way to mitigate it but because it’s two separate email conversations, I am not optimistic.  Again, this should be a non-issue for any / all tickets moving forward.