Prior to my retirement, Visio was 50% of my workload. Nowadays, I have to rely on memory to offer potential solutions (I no longer have access to Visio). With that in mind...

When you create an object on a particular layer does not mean other objects from other stencils belong to that layer as well. They have to be assigned to that layer. So, when you moved a flowchart item from the stencil to your drawing, it will only keep the layers that it was assigned when developed. Now, you can highlight the item and assign it to another layer if you wished but, I don't know your intentions.

Sorry this may be a lil sketchy but, I know this board has little activity and wanted to respond. Maybe this will jog the minds of other Visio users to assist.