Congrats on getting this thing somewhat figured out. I found the same problem as you where links to hard buttons disappeared after uploading a NCF file. The same phenomena happens if you close out of a file that appears to have all the links working, then re-open it. After opening it, some links are gone!

It seems to me that hard buttons linked to other hard buttons is the problem. What I did is this:

1. Create soft buttons for all the hard buttons used in each device.
2. Learned those soft buttons from the original remotes.
3. Created links from the hard buttons to the appropriate soft buttons.

So if I need to link to say a TV's volume Up and Down buttons from another device, I link to the soft buttons learned in the TV device (not the TV's hard buttons). This proved to work the way we expect it to.

Always a work-a-round, never a fix...I always say!

By the way, it took me about 10 hours of really concentrating on what I was doing to finally get the hang of this thing and complete a configuration. AND I am VERY familiar with the big brother remotes. After all was said and done, I actually like this thing very much from a every day use stand point (once finally configured).