frozen-bubble-client has the sdl patch not applied, because of the behavior of
patch.
I saw in the ebuild that frozen-bubble is symlinked to frozen-bubble-client.
When now the patch is applied. The patch command moves frozen-bubble (the
symlink) to frozen-bubble.orig (so the symlink is renamed) and makes a copy of
frozen-bubble-client in the (now regular) file of frozen-bubble. So if you
remove frozen-bubble afterwards in your ebuild _the patched file_ is removed.
Make a simple mv or so as a solution.