I've only changed Mac mini HD once, but it went well without problems. Real HD to a bigger real HD.

I backupped my old installation to an SFS formatted USB drive (use MirrorCopy or BackUp or similar which can preserve softlinks from SDK etc), swapped the HD, and then I was too lazy to make new partitions manually and booted from MorphOS installation media and let it make the partitions automatically, and then I formatted the fresh installation/partition and copied my backup back to the new partitions (with a proper tool again).