Since Aatrix allows you to file 2015 W-2's after the year is closed, one would assume that ACA forms would work the same way. Since this could be a faulty assumption, we still always recommend that PR files are copied to a backup company BEFORE the year is closed.
If you run ACA forms from the backup company, this does mean that ACA data may only be in the backup company code. ACA data is kept by year and the files use the new Sage structure (see attached) so you could possibly copy them into the main company code. This would need to be tested.
Other options for getting ACA data from a backup company into the main company include 1) use VI to export and import 2) use our ACA Data Assist tool that can import data into any company code. Since ACA data is kept by year, you may never need to copy back to the main company code if ACA forms are processed from a backup of PR.