Debian uses udev. Udev handles mapping MAC’s to the appropriate /dev/eth(X) file. If you copy a Virtual machine, Udev will remember the MAC address of the old NIC. When you copy the machine, the virtual host usually generates a new MAC address for the VM.
Udev will assign the new Device to eth1, eth2, and so on. If you want to change your NIC assignments make Udev forget the old MAC.
In Debian 5 (lenny) it is in this file:

/etc/udev/rules.d/70-persistent-net.rules

In Debian 4 (etch) it is in this file:

/etc/udev/rules.d/z25_persistent-net.rules

To apply changes in Lenny: “udevadm trigger” or “udevtrigger” (in Etch)

I know I did this the hard way. there is a command that you can issue that will convert them on the fly. what I did was mysqldump the database, reinstall mysql(because of other reasons), and then edit the dump so that the line that specified the engine reads “ENGINE=INNODB” instead of “ENGINE=MyISAM”.Then I imported the dump.

I was getting annoyed that when listing my tables in phpmyadmin,  it would show the list of tables in InnoDB (which is what i wanted), but then, when showing the summary at the bottom of the page, said “MyIsam”. I easily got rid of it by adding “default-storage-engine=InnoDB” to my “my.cnf” file.

when running an update:
sudo aptitude
Ouch!  Got SIGSEGV, dying..

apparently, just remove some files:
sudo rm /var/cache/apt/*.bin

now everything is back to normal.