I just noticed this topic and thought I'd chime in.
Periodically, I like to refresh my library to get the latest updates from MB. My library is basically organized this way:
Letter of AlbumArtist (e.g., 0-9, A-Z, and [Various Artist]) / Artist / Album / Tracks
So, when I refresh, I will usually do a whole "letter" at a time (e.g., all the "A" artists). This works great and I can do a letter or a few in an evening. I create a dummy directory to mark where I am (e.g., "A - complete") and just move it along when I have time.
I use the Remove Perfect Albums plugin - it works great, but I have noticed a different issue. If none of the Metadata has changed, but the artwork has, it still shows as unchanged! Due to this, I usually just re-save the albums even if they do not show changes.
As for the 503 (albums not loading), what I have been doing to cope with it until the servers are updated is to sort by the album name - they all go to the top or bottom, then select them all and hit Ctrl-R to reload them. It works pretty well, but if the servers are busy, it can take several passes to get every one.