If MB is set to continuously monitor the folder of the files in question, it will pick up the tag changes on the fly. or on startup if that option is selected, or manually via Rescan Files. However, changing the filenames with an application outside of MB will NOT be picked up. Filenames need to be changed within/by MB itself for them to be changed in the library itself, or else they are treated as entirely new files and pre-name change ones will still show up, as "Missing". Yes those "missing" entries can be removed with the "Compress Library" function (Tools/Advanced), but..
If you are going to do a whole editing job on all your files as you describe, the best solution might be to first do all your Mp3Tag work outside of MB, then have MB create a whole new library based on the results, deleting the old library afterwards.
frankz beat me to it but take this as a +1 to what he said.