Is there any coating that can be applied to protect the wood such as polyurethane, and how would this affect the sound? Supposedly Jaco Pastorious used boat epoxy on his fretless bass.

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Various epoxy and Cyanoacrylate (super glue) finishes have been used on fretless fingerboards. This tends to yield a brighter tone and may wear longer than bare wood, depending on the material used. Some such finishes do not adhere well to oily woods such as rosewood or pau ferro. Have an experienced guitar tech do the work!