If I remove pages at the front and back of a document, images may shift positions. I use the sectioning feature to assure that page numbers and positons don't move but for some reason images may shift up or down in layers or move to different pages. I can't think of any reason this should happen.
Version of ID? Is the latest patch installed? Are the images free-floating, snapped to guides, anchored, on the master page? We need some more details, and some screen shots of before and after would be useful.