Just because I am picky, you probably mean copy and paste, right?

Double-click on a button that you are trying to copy from, and see how it is labeled. If it is a learned command, or a command from the database (you made a beginner oops - you did not tell us what model number the remote is), or if it is aliased to a command somewhere else.

If it is a database command, you can't copy it because pushing the button tells the remote to look in its memory for a command, then issue it; the database cannot be copied.

If it is an aliased command, you are copying a button that says "go do that over there" so you have to copy "over there at the same time in order to have it work. If you don't, the command will just be a blank button.

If it is a learned command and this is happening, then and only then do you have a problem.

Again, about the merge, what model number(s) do you have? If you are merging files, I think the one that is merged (i.e. opened second, then merged) will not bring in commands if they are database commands.