You have to make sure it's built against the same version of the firmware as you are using.
There's not really much point in deleting the unused protocol files. They live in the file system space, which isn't really an issue yet. I suspect they'd still show up in the list of protocols, and you'd just crash the Tx when you tried to load them. or maybe you'd get a failure warning - I haven't checked the code.
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My remotely piloted vehicle ("drone") is a yacht.