Right now, there is a limitation in CMA that it does not delete records on the target environment. This limitation is documented in the CCS Help:
This is causing issue when importing Rate Calculation Groups where some of the child Calculation Rules has been deleted from the source environment. This will result in duplicate Calculation Rules with the same sequence.
SOURCE
TARGET
This causes the CMA Import to become less efficient as the deployment manager will need to manually delete all the records that were removed from the source environment.