My brother just got done doing a 5 or so trimming and seperating of his java ferns and i can tell you from experience you can do very little wrong.
To give you an example, in my tank now, i have an about 2 inch root that came off one of the plants that is sprouting leaves! so even roots can come back. I've also have a few that got cut a bit (by what i don't remeber) but about 6 little plants spawned from the cuts, so even there you'll
As far as the little plants, you can take them off at any time, but a bit bigger and they seem to grow better, so i tend to leave them on till they have a few 1-1.5 inch leaves on them.
At anyrate, you can't really kill it very easily so go for what you feel like.
-Lady Astor: "Winston, if I were your wife I'd put poison in your coffee."
-Winston Churchill: "Nancy, if I were your husband I'd drink it."