OK, though you don't give a lot of info. Assuming the codebase does not have bugs with this I would say if the changes don't take, you are not writing the changes to the file the MUD is loading. When you foldarea does it tell you the area is saved? Is this an installed area that is saved in the area dir and that same filename is in the area list? (I have seen issues where using savearea on an installed area writes the file to the building dir, there might be a related issue with foldarea with proto areas). Is the object you are editing actually in the area you are saving? Though you imply the object does load, but not with changes, just in case the object does not load at all, does the high/low object vnum range of the area include the vnum of the object? There could be other issues, but I would check these, and you can see if the change is in the file by directly looking at the area file.
It's worth noting that almost any code of any significant size cannot possibly be bug free, although it might certainly be free of obvious, easily avoided bugs.
From reading this -> http://www.realmsofdespair.com/smaug/her... I assume you are intending to set the prototype flag on an object, modify the object, reset the flag (i.e. 'clear' it), then save the area to preserve the changes to the object.
It is usually a good idea to use foldarea twice, once to save the file and a second time to overwrite the backup file.
Maybe that might make a difference? I can't see the messages you get, so I assume you assigned the area to yourself beforehand? Do you have two copies of the item (created before change, created after change) to verify that this worked 'across the board' as you say it is? Can you tell that you successfully set the prototype flag?