Has anyone ever encountered this in Federal Court?

Hello everyone! I had posted a little while back about service concerns on a FTCA case filed in the Middle District of PA against the US, a facility, and three individual healthcare workers. Well, everything wound up going smoothly, but after a conversation yesterday with defense regarding our joint case management plan, it has now gotten more complicated and we are facing something I've never encountered before.

So we are alleging negligence from 2014 on. However, it's now been brought to our attention that the specific facility we've brought into the action did not actually become a FQHC until 2015. Because of this, defense does not think they should proceed with dropping the individual/facility defendants (leaving only the US), and instead move forward treating the case as two separate actions within the same action? Essentially, we are going to have a "pre FQHC" (against the facility and individuals) and "post FQHC" (involving them and the US).

We have NEVER done anything like this before, and to make it better, defense has admitted this will also be the first time they are doing it, so we are all going into this green. Have any of you ever had a case like this, and if so, how in the world does it work? I have been trying to research what I can but I would like to hear how this goes in practice.

Also, for reference, we did not know this before we filed our complaint (in December), and the statute has now passed. Defense has just now read through our entire complaint and this is why we're just finding this out.