Since I began using Dynamo in December, I have noticed something mildly frustrating. Sometimes copy and paste between Dynamo graphs (.dyn files) does not work. Since update 0.7.5 this seems to function better though.
I have began to utilize a silly but simple solution to fix this. I simply created a custom node named placeholder and I copy/paste what I need into it each time I need to save the layouts.
Since a .dyf and .dyn can be opened simultaneously this seems to work perfectly. See the video below to see my method in action.