The correct way to remove a part is remove it from the bin inside FZ, otherwise you have to search and chase instance inside the file system.
Yeah you didn't follow the FZ layer rules for PCBs. Go watch my PCB video if this doesn't make sense.
You make a group called silkscreen and put all lines and text in it.
Make a group below that called copper1(top copper), and in that make copper0(bottom copper), and in that put all contacts. With round contacts the OD is the size of the pad, and the ID is the size of the hole.
If this part will be fitted to a custom PCB that you are making, make the header pins 3mm apart and just install individual pins in each hole.