That's still not that hard to work out.

So if it won't scroll, here's the idea expanded for different map subsections:
You store the X/Y coordinates of the boulder AND X/Y coordinates of the subsection and edit when appropriate.
Boulders don't appear on the main world map iirc, only in dungeons. Leaving the cave would obviously reset the boulder coordinates, no problem at all!

If it does scroll:
Same thing, just edit it a little.

Come one, you're the master coder, not me

Just have a Boulder be a special NPC that loads on the map after the main map loads. When you're coordinates overlap, the Boulder is shifted.
I did the same thing in my VERY old WoM walking demo; it isn't that hard.  

Woot nice!  

And for that there's Onblock or whatever it was called