A) You can remove the dunbrack binary at any time; Rosetta should automatically regenerate it. The binary contains no calculation; it just exists to speed loading (usually 30 seconds for text, versus 0.1 for binary).
The file permission is at issue if it ALWAYS has to load from text. If the binary exists, I don’t think it’s the issue.
C) You should try using the PackerTask option for input sidechains. It’s use_input_sc or include_current or something similar. That will leave the native sidechains as allowed rotamers; if your score does NOT increase it may mean that you have many off-rotamer sidechains in your input that Rosetta can’t find when packing.