A better way to use MobileSync with GoodReader?

As I said, this is just my own way of doing things. Work out what makes sense for yourself. Good luck with that.

You’ll never get labels syncing with anything else the way you’re envisioning. Labels and tags are fragile attributes and there are no reliable, universal, programming standards that you can rely on to build a rock-solid workflow. Consider using prefixes or suffixes on your document names, changing the prefix/suffix string to reflect status.

Read Help at goodiware.com. Perhaps adjust the sync settings on that folder. E.g.,