I use an external to clone with CCC. I believe there is an option in CCC to NOT delete things from the external that are not on the internal. That would accomplish what you want. The way I do it, however, is that I have partitioned my external into two partitions. One I call "Clone" and it is the same size as my PB internal drive. The other partition I called "Other Files". That is where I keep my music and photos so they don't use up all my internal space. You could do something similar and simply keep the files you don't want to lose on a separate partition. Disk Utility will partition the drive easily. You will, however, lose the clone you already have on the external, but after the partitioning, you can simply do another clone and all will be well.
Good luck!