Syncing directory with thousands of files

[MxxCon]

flashfxp will also list each dir...
what you can do to speed up this whole process is you can queue up instead of root dir of your project, but some levels down. this can cut your transfer time ~50-80%
try some shareware/freeware download sites..i'm sure they have some dir sync soft. i haven't used any of those so i can't say if they are any good.