Fix custom_apns script

Removing an element from the list that is currently iterated does not
work. At least it may skip the next element.

Also the handling of duplicate APN names was broken: It would output the
lines containing duplicate APN names times the number of the
duplication, i.e. the exact same line would be duplicated.
So use a `set` for storing apn names.

Change-Id: Id54d245dc935117cd4640ae0f1f30b8608c87459