I am pretty sure it does, because when you give someone the opportunity to reload the source code than the "main code" should be burned in memory as well.
However, if you want to make sure, the put the burn option in your ladder code. You simply have to set SB 372 and the current code will be burned into flash memory. I used to set SB 372 in my codes when the user did certain changes in a configuration menu, especially when changing timer presets. Why? When you use the burn option in VisiLogic than "your" preset-value will be stored in memory. But I found out that if you set SB 372 manually in your code then code will be burned to flash memory with the current timer-preset values at least on Samba PLCs), So, the changes to timer-presets are part of the backup then.