OK. I may be tilting at windmills with this question as asked.
So I tried generating a 10000x10000 and layering a 2000x2000 multiple times. Then merged them all down.
Saving this (as png) created a 31,586 KB file.
Closed Paint and re-opened. When I try dragging, etc, it seems to render the components of each block, somewhat in the order they were created.
Closed Paint and re-opened. Without change, I saved as jpg. That created a 3,296 KB file. Nothing unexpected here.
Closed Paint and opened the jpg file. Without change, I saved as png again. That created a 7,277 KB file. And here is the surprise. That's 25% of the original. SO, what has been "compressed" or "lost" in the transition? The rendering now seems to be related to blocks around my cursor, quite different to the original experience.
So, it may be that I asked the wrong question. There is a significant difference between the png file created by layering and merging (particularly as I ensured that I had layers overlapping), and that created by converting to jpg and back.
I am wondering what that difference and whether there is a method to "resequence" or "discard rubbish" without performing the double conversion.