Yes, this is totally fine. I suggest that you move the files from within MB, though, so that it doesn't lose track of them. Right click > send to > folder (move). (Try this on a few tracks first to make sure it's working as desired. Then you can do the whole library at once or in batches, whatever works best for you. Also, if you use auto-organize, you will need to use those settings to reorganize, or turn it off and then reorganize.)