So you have an inbox of 4.1Gb and 3300 messages. It is absolutely no
wonder at all that things are taking a long time. A 4Gb mbox file is
huge, massively huge. Every operation involving mail in that file will
generally need the file to be copied (and modified while copying), the
old one deleted and the new one renamed - copying a 4Gb file takes a
significant amount of time, never mind the processing that has to
happen with it. It is for precisely this reason that the mbox format
was dropped.