In VPOP3 v6.6 and earlier, Lua scripts are stored as separate files in the VPOP3 installation directory. If you wanted to back them up you would need to copy them separately, and they had to be edited from outside VPOP3.
In v6.7 and later, they are stored in the VPOP3 database, so that they are backed up/moved/etc along with everything else, and so that you can edit them from within VPOP3 itself in Settings -> Scripts.
If you make a Lua script file in the VPOP3 directory, then VPOP3 will import it into the database on first use, and rename the Lua script file to a .old file so that it does not have to be checked and imported every time the script is accessed.
So, in v6.7 and later, generally do not use .Lua script files in the VPOP3 directory, but edit them from Settings -> Scripts.
If you want to delete a Lua script, simply empty the script in Settings -> Scripts.