I created a coverage layer ( polygon) for an atlas. It contains rectangle polygons which define the boundary of sheets (somehow irregular indexing along my layer). when I print the atlas without changing the scale of my map (scale 1:1600), I have the same overlap that I defined in my coverage layer (sheets polygon). But when I force to map to specific scale (1:1000) I lose the overlaps between the sheets. How can I change the coverage layer scale to 1:1000?
The scale of your map items is controlled by the size of your coverage polygons. Figure out what size polygon will give the desired scale on the size page you'll be printing. You can find this by setting the print composer map to the desired scale, then looking at the map's extent (under item properties).
Then resize the polygons in your coverage layer to that size. It may be easiest to create one polygon of the correct size, then copy-paste that polygon and move it to the desired locations.
Generate an atlas at either a fixed scale or zoomed to the coverage layer with a 0% margin. These setting should now give nearly identical results.