Hello,
I have extensive experience with MySQL and have recently performed a number of similar tasks to your project, of dumping the data, deleting the old data and reloading the data.
I am presuming you may be referring to the ibdata1 file growing exponentially? If this is the case and you are using innodb tables, then I can also help you to modify some settings to keep the problem from occurring in the future.
If you would like to contact me with some further details, we can clarify the project, make a plan and go from there.
Thank you.