At the moment, in version 2015, the license is checked out whenever a DFT calculation starts, and then checked back in when it's done. For DFT-MD, it means the license is checked in/out several times while the script is running.
In 2016 this will change, so all licenses needed will be checked out in the beginning of the script.
On the other hand it doesn't matter so much for nodelocked licenses, if that's what you have, since there is effectively no "count" in these, i.e. you have infinitely many licenses for each available feature in the license file - but of course these can only be used on that particular node.
This discussion may be better continued on the support@ channel, then we can be more specific regarding your particular licenses.