Also, what about the old patches on the server? Can I delete those without problems?
Yes, you can delete those.
Can I simply delete them without adjusting the wyBuild project file? I actually want to only generate a patch from the oldest deployed version and a catch-all patch for everything else.
Well, wyBuild isn't really designed to work that way. What's the problem with creating patches for all your versions? Would you rather have incremental patches (e.g. A -> B -> C instead of A -> C, B -> C)?