I have a section in my shop that I use to highlight certain items each month. To do this I use the import feature and bring them in from my other sections. I thought this was what you were supposed to do, but someone said they create a duplicate item.

My question is this? Does deleting these secondary items mess up affiliate sales somehow? How do you create temporary highlighted sections without messing anyone up?

Also what about moving sub-sections and products, like if a certain section just gets too big and you think it would be easier for people to find designs in 2 sections instead?

Anytime you delete a product or design you potentially create problems for those who have linked to them. Moving does not create duplicates. Importing creates duplicates.
http://tutortanith.com/shoptips1.htm#avoiddups