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First: Old leaves don't "repair" so changes will happen only to the new ones.
The condition is fairly normal for Java Fern. Mostly I believe a result of rough
handling at some point or exposure to air while moving/during planting.
Any Java Fern I've had has had this till new leaves came out so I could remove the old ones. The leaves also tend to just stay longer as the result of the slow growth rate of
this plant so when fine algae forms on the older leaves, snails often eat this and don't
necessarilly stop when they get to the bottom of the algae.
I wouldn't trim any yet as the plant is still getting light through them. Especially that
big main one. After a fully developed leaf gets there you can trim off the worst one
and so on. I suspect that(at most) this plant has been in there for 2-3 months.
Because they get nutrients from the water, using Macro/Micro ferts is more important
to this plant as they can't get benefits from root tabs(unless you put it where some of the roots went into the sub).
 

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Plant Whisperer
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Java ferns just tend to develop old ratty looking leaves like this. I don't see any reason to cut them at the moment, they still function and help the plant gather energy.
 
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