Mobs (and possably other entities) that went through a nether portal cannot be targeted by any command.
If a player executes the command, The console says 'That entity cannot be found'.
If the command is executed by a command block, the entity is just silently ignored.
The command I used was '/kill @e[type=Skeleton]'. As seen in the screenshots, none of the wither skeletons that went to the overworld are killed by the command.