Pretty much since I've had this site back up I've had two copies of the thing locally. This is obviously well redundant, but was driven by me wanting to use BBEDIT's Site Syntax Checker. If I'd just run it through my Nanoblogger directory it would be checking a load of folders I don' want it to (i.e. metadata files, databases, caches, etc used to generate the blog) and would generate a shed load of errors. So instead I synced a local copy of just the blog so I could check it all easily and also upload more easily.
BBEDIT does offer a tool for skipping certain directories when checking Site Syntax, but these directories have to be enclosed in brackets/parentheses. I finally figured out how to alter Nanoblogger enough (config.sh - wasn't that hard, I just hadn't had time to look) so that I could do this. So now it's all a lot neater my end with just one copy of my site.
Then I just altered my upload command:
find . -newer .lastupload \! \( -name ".*" -or -path "*(*" -or -name "blog.conf" \) -type f -print | cpio -pdumv /Volumes/myidisk
touch .lastupload
Lovely