No, nothing should have moved, everything was kept the same, just in the data directory instead of the install directory to maintain compatibility with old maps. Sometimes the same fill are part of several add-ons though, and sometimes it's just the same name, but completely different fills. The name "Wall Cobble Grey" isn't particularly unique, lots of dungeon styles include grey cobble walls, but they still differ in style.

In this particular case, I guess it was distributed with both add-ons, because an owner of Perspectives 3 isn't guaranteed to have DD3. I have everything installed, and I have that file in both those locations.

Note that unless you actually edit the actual bitmaps to make your own variation of the originals, you shouldn't copy the official files to other folders. That's just going to put in into trouble the next time you are viewing the map on a new computer since you will also need to recreate your copied folders exactly as before as well, instead of just relying on the installer putting things right (and it will also prevent others opening the map properly if you ever give someone the map file.)

Check my recent blog article, it describes ways to fix Red X's.

Do note that moving the files to the installation directory is not really a good idea, the setup with the data files in a separate directory is for a good reason. Also, maps that uses the old relative paths (starting with # meaning installation directory) should also automatically be redirected to the data directory, so it may indicate that your map didn't use proper CC3 paths in the first place, so fixing the path sin the map is a better option for the future compared to moving the files, even though it may take more effort.

True. You don't need much snow before any resemblance of the roof structure is completely gone.

You can do mass replace from the symbol manager. Just pick the symbol to replace, and then pick the one to replace it with. Note that the symbol you wish to replace with already have to be placed in the map once, otherwise it won't be in the symbol manager list.

Note that you can only replace one symbol type at a time, there isn't a way to simply replace varicolor to non-varicolor.