One thing you might want to do is to keep from modifying the atime on the 
source files. Perhaps mounting the source volume as read-only could do it, 
but that might not be feasible. AFAIK, the Linux EXT filesystem is very 
slow in deleting files, so perhaps copying them all first and then 
deleting the originals later might work. Maybe someone mentioned that 
already.

I have copied some filesystems considerably larger than 100GB, but maybe 
not with 1.3 million files, and it's not taken days. Perhaps several 
hours. And this not with fast machines, either.

Maybe, for the future, some of the applications that create a bunch of 
small files can be made to create them under a tree that is a filesystem 
inside a file on another filesystem. Then, you just unmount the inner 
filesystem and copy it from the master filesystem to a filesystem on a new 
device or machine, and then remount it. So you're not actually making new 
inodes and directories when you copy.

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