Because it was in RAM but not written to flash ROM.
When you send the update, it boots into the "nanoloop" screen. Nanoloop then is in GBA RAM as it would be when booted from the cart. To actually write it to the cart, you need to hold B and press START+SEELCT (while still holding B) which brings up a message "UPDATING ROM" with a progress bar and automatically reboots the GBA after a few seconds. If it does not show the update screen and reboot but just starts nanoloop instead, you have not pressed B first and the update procedure has to be repeated from the beginning.
Maybe I should change the key combo so that select / start are not involved and you can't start nanoloop by accident.
To get familiar with it, you can perform the write-to-flash operation when starting from the cart, too: When you see the nanoloop logo, press B+START+SELECT so that the update screen appears. Nanoloop will write itself from RAM to ROM, e.g. do nothing.