You can use ioNiNJA to rescan an entire tree with 'site rescan all'. If you want to only do a subset of the things in a directory use a macro in your client. With FlashFXP:
Code:
{
cwd %f
site rescan all
cwd ..
}
Then you can highlight the dirs (normally just plain dirs but some might have Disk1, Cd1, etc under them) and run the macro over them. Seems to work OK for me.