Java fern will be fine. The leaves will either green up again, or it will put out new leaves. I take off the shoots from mine all the time and move them to different tanks. They frequently stress out due to the changing water parameters. I actually had some that looked sickly like yours and I converted the tank to brackish over about a week at 1.007 SG for my opae ula. The ferns weathered the change and have greened up considerably. I plan to ultimately get the tank to 1.009 or 1.010.
Sorry about your fish. I'd be surprised if it was the Excel, but stranger things have happened.