They are two things that can be good for you in this instance

• GOOD THING #1 : You can convert the two MyISAM tables to InnoDB
• GOOD THING #2 : The two MyISAM tables are never changing

If either one of these good things apply, then I have good news for you

STEP01) Zap All Binary Logs on the Master (OPTIONAL)

Run this command on the Master:

mysql> RESET MASTER;

If this part scares you, you could either skip it or make a copy of the binary logs before doing it

STEP02) Create the mysqldump as follows:

echo "STOP SLAVE;" > MySQLSlaveReload.sql
mysqldump -v --master-data=1 --single-transaction --routines ....  >> MySQLSlaveReload.sql
echo "START SLAVE;" >> MySQLSlaveReload.sql

STEP03) Move the MySQLSlaveReload.sql to the Slave

STEP04) Load MySQLSlaveReload.sql on the Slave

On the Slave, load the script as follows:

mysql -u... -p... -A < MySQLSlaveReload.sql

The script will stop the slave, load the data, and start the slave. What about the log file and position? Before you do STEP02, look at line 22 of MySQLSlaveReload.sql

head -22 MySQLSlaveReload.sql | tail -1

The mysqldump option --master-data=1 recorded the log file and position as of the start of the mysqldump on line 22.

Give it a Try !!!

I found the question relevant, however it is answered before elsewhere

1. You want to turn off you database (take the backup, but only for the reason of having a backup)
2. Go to you config file (.ini), in there locate the datadir
3. take a copy of this directory, or make sure it is not removed when reinstalling
4. Reinstall, and check if everything works, make sure the datadir is the same

This is how i would do it, but i haven't tested this, so you might bump into issues

(this idea/theory is backup up by this guy) http://dacosta9.wordpress.com/2008/10/25/moving-data-files-to-another-disklocation-mysql-sql-server/

And from Server fault https://serverfault.com/questions/68146