Strangely enough I didn't had any issues, but the testing I did was simple and small mind you.
I created a test game with one map and a treasure chest, I made a copy of that game, in the copy I added a new map and item in another treasure chest.
Then I played the first one and saved. I copied the files (maps, RPG_RT.exe, RPG_RT.lmt, RPG_RT.ldb) from the second one into the first ones folder and played it, the save worked and I was able to move between maps and get the new item.
That's the small test. What you should do is make a copy of your game and name it something else, play a few hours and keep the saves, then keep on working on the original game files, when you think it's different enough then copy the new files to the copy game and check if everything works.
I'd advise you to PM Kentona about his patch, that may shed some light on the issue.