burnt fingers with IMAP

R wanted a solution to back up his gmail. Suggested IMAP, since so much is said about IMAP being superior to POP3. But in this case,

1. His total email size is going to be more than 4 GB, and according to Murphy's law, he will probably be still on FAT32, so will crash when that happens.
2. Archiving to DVD and deleting old mbox files will probably cause catastrophe with IMAP - won't that delete files on the server?

So, recommended POP3 to him. But he needs to make a lot of filters to make folders and populate them to recreate the labels he has on gmail.