Here is another idea: Instead of trying to automatically detect orders merged on the eBay website (with all performance and consistency issue), how about a “Detect Combined Orders” command in the menu of GarageSale.
You you would need to manually invoke the new command after having used the “Combine Orders” feature on the eBay website, and GarageSale would try to do the matching only then.
It would not be as convenient as automatic-detection, but it would drastically reduce the possibility of us causing problems for everyone, since it would probably take a few iterations until the feature works without flaws.