Thanks, Walter - I'll save this for future reference in case I get a repeat of this issue. In the meantime I dealt with it by deleting the huge folder from Dropbox, which proved something of a mission itself - I had to stop syncing on both machines, wait for the folder to delete, unlink DB, delete the mirrored folders on both PCs, reboot and relink, and then the remaining folders synced as normal. We're back to real time syncing again now.
The actual cause is still a mystery, since the million-file folder (and subfolders) has always been there, so it wasn't something new we'd set up.
When I first tried deleting the folder on DB, I forgot about the two-way syncing, so it was trying to upload all the files from the PC again once they'd been deleted from the web folder. Curiously, the local folder I'd unchecked under selective sync to stop this happening had become automatically checked again somewhere along the way!