I can't explain anything about CentrED+, but i did do some CentrED before.
You don't have to take your shard down to edit the map; that is if your CentrED isn't using the server's original files directly.
I would recommend hosting the CentrED servers on a different new folder with a copy of the server mul files, to avoid messing with the original map and to be able to map and have the server opened at the same time.
As for the deco ingame, i am certain they will remain as is; what you placed ingame are most likely unfrozen statics, which means they won't even appear in CentrED.
You can freeze and unfreeze items using [freeze and [unfreeze respectively ingame.
Be warned that it will save/remove them from the server files directly, you will hav eto update your CentrED map with the new mul file, erasing potential changes you have made in CentrED.
What i suggest is that you freeze/unfreeze what you need before donig changes to the map, then copying the mul files to the CentrED files, doing the changes, and putting it back in the server files when done. Your clients will have to be updated with the new server mul files as well so they can see the changes.
Player houses are multis, they aren't frozen in the static files.