Assemblies that have some movement, such as a hydraulic cylinder or hinge, are by default rigid when inserted into another assembly, but they can be made flexible. Find the sub-assembly in the upper-level assembly tree and click on it. Choose the "Make Component Flexible" icon. It should now have the same amount of freedom that it had in it's own file.
I believe this icon was first available with SW 2014. If you're using an earlier version you will need to choose the “Component Properties…” icon instead.
That will take you to the Component Properties dialog box. “Rigid” will be selected by default in the “Solve as” section. Select “Flexible” instead, then “OK”.
By the way, if you have a Limit Mate in your sub-assembly it may be broken when you insert it into the main assembly. If that happens, delete the Limit Mate from the sub-assembly and apply it in the top level assembly instead. I rarely use Limit Mates, but I have seen reports on the Forum that this was much improved with SW2016, so if you're using 2016 or later you might give it a try.