Existe uma opção --max-size para o rsync, que excluirá arquivos de um determinado tamanho de serem copiados de um diretório para outro. Da página do manual;
--max-size=SIZE This tells rsync to avoid transferring any file that is larger than the specified SIZE. The SIZE value can be suffixed with a string to indicate a size multiplier, and may be a fractional value (e.g. lq--max-size=1.5mrq). This option is a transfer rule, not an exclude, so it doesn't affect the data that goes into the file-lists, and thus it doesn't affect deletions. It just limits the files that the receiver requests to be transferred. The suffixes are as follows: lqKrq (or lqKiBrq) is a kibibyte (1024), lqMrq (or lqMiBrq) is a mebibyte (1024*1024), and lqGrq (or lqGiBrq) is a gibibyte (1024*1024*1024). If you want the multiplier to be 1000 instead of 1024, use lqKBrq, lqMBrq, or lqGBrq. (Note: lower-case is also accepted for all values.) Finally, if the suffix ends in either lq+1rq or lq-1rq, the value will be offset by one byte in the indicated direction. Examples: --max-size=1.5mb-1 is 1499999 bytes, and --max-size=2g+1 is 2147483649 bytes.