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I've found Java ferns to be very durable. So even if they look a little rough, as long as the rhizome is hard and alive (not mushy) with some care they'll make a comeback. Unfortunately, it takes time since they're not fast growers. I've heard that you can cut the rhizome and that may motivate the Java ferns to sprout new leaves. I know this works with Anubias as they always come back even bushier when ever I trim them.

Having the plants closer to the surface is usually a good thing, they get lots of air exchange and they're closer to the light. This usually speeds up their growth. However, you still need to keep the water parameters in mind - some GH and nutrients in the water column will help with their health.

Otherwise, you can always use other plants such as anubias (also slow growing), hygrophila pinnatifida, or a nice moss such as fissidens, weeping moss, or coral moss to get that riparium affect.
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