Nether trees will overwrite any redstone component that is not a full block when grown from a fungi. It just deletes them.

I have tested it with redstone torches, redstone dust, hoppers, pistons (both kinds as well as extended), repeaters, comparators, levers, buttons, pressure plates, trip wire hooks, string, daylight sensors and rails (all kinds) and they are all deleted by nether trees growing.

This is very annoying and would be awesome if it is fixed soon.