About the deletion: What I mean is the full clipboard history. After "merging" sometimes there is only one item left in the "history", which contains the merged last two items, but the others are gone. In my eyes, the clipboard history can never be empty (or contain only one item) on a computer where the user works with the clipboard (and who doesn't?). It should always have the maximum number of items, which accumulate there until overwritten with newer ones.
As to the hotkey, I don't know how Alfred handles this internally. What I meant is that _merging_ should have a separate hotkey, not "normal" copying. I think this should be possible, as Alfred could be made to act on the clipboard content after any keystroke. Similarly to alt-cmd-C which displays the history, e.g. cmd-< could trigger merging, couldn't it? As a solution I could think of:
cmd-< (or whatever the user chooses) emulates one cmd-C to get the marked text and put it into the clipboard, then merge the first and the second item in the clipboard, and write the result back to the clipboard and the history.
Of course I could just switch off the merging (that's the workaround I am using right now), but isn't it a pity to give up
a nice and useful feature of Alfred just because the interplay with another program is a bit tricky to handle?