Richard,
It looks to me that the "Target Connections", which holds the target configurations, is the key to your problem. This can be used to overwrite the RCW during debugging... Of course, you'll probably need to figure out how to make it permanent (probably by using the configuration project - something I'm playing with right now).
I duplicated the existing LS1046A_RDB configuration, and named it LS1046A_RDB(1)

I set it up to used the LS1046A processor, and set it's IP address, and used the "little flashlight" icon at the top right to verify connectivity:

Then, I modified the initialization script by setting the flag USE_SAFE_RCW to "True":

In the README tab at the bottom, there's a lot of useful information about this RDB...
Anyway, after saving this Target Connection, and making sure it was being used in my debugging session (by selecting it in the Debug Configurations, under Debugger tab), the debugger should be using the default RCW instead of the corrupted one (or non-existent in your case):

At least, that's how I'm reading it...