Installing fault indicators is no big deal and they should be present in every transformer lokkin at the next transformer in the circuit.. If you get a flag it simply means fault current passed thru the indicator.At some point you will see one indicator with a flag and the next one normal. Your fault lies between these two.And you must always bear in mind that the fault could be a transformer rather than a faulted cable.
The only other method I am aware of is to isolate every transformer . refuse the lateral and start pluging them in one at a time until you blow the lateral fuse again. This process can be quite lengthy and is less than desirable. If you have lots of URD construction I would try and push for fault indicators to be installed at the same time the transformers are put in service..
You didnt mention what primary voltage this was But On voltages of 20 kv and higher I would feel safer with at least 2 men being involved with the actual switching.