I have this problem in 2014 and it's also happening in 2015 now.
It has been brougth to attention to Autodesk (Andy and Nick) but it's very hard to get it exactly reproduced and find out what causes it.
It just happens. Putting the subassembly back in resolves it, but it happens again randomly. For now i have found no way to predict the behaviour.
Since it does happen on a regalar base, I am wondering whether anybody else has this problem also.
Jaap.
(PS: it's a issue that is occuring a long time. It was also present in the 2013 and 2012 versions, and probably even earlier)
Just stumbled across this post and was wondering if you ever found a solution. I am having this issue with Fabrication 2015.
The issue is under investigation by Autodesk. I have been able to replicate, and based on that, so is Autodesk.
There is no solution yet (in 2015), and I haven't checked in 2016 yet. However, there is a workaround (better, a way to prevent it from happening).
This problem can (not always!) occur when you use F2E (or the old Fill) from or to a subassembly. So, dont use F2E in that specific instance and you will be fine. Put a normal duct first, fill that out, and then replace that with the subassembly.
It is some extra work, but it will prevent the disappearing.