I'm not familiar with exactly how the barrel systems on your side of the actually work. But if you can introduce fresh co2 into it without 1) infecting the beer, 2) agitating it in such a way that it would oxydize and stale, the yes, go ahead!
I assume it's like what he's showing at 5:39 in this video, if that's the case, and all you're doing is charging with a fresh "cartridge" then you'll be fine.
[ame]https://www.youtube.com/watch?v=l4bkkrE2zEU&t=5m39s[/ame]
(I tried to post this with that start but it didn't work.)
If you're talking about installing the carbonator cap first, you should still be ok, but make sure you sanitize the cap first, and also around the threads and top of the barrel. You also may degass what's already in there, so you might need two co2 chargers.
But if you're careful and sanitary you should be fine.