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Ah - the auto-connect is what I missed! So I reckon that for an existing session, in my .qtr file I should change
<auto-connect>1</auto-connect>
to
<auto-connect>0</auto-connect>
and then delete the relevant parts of the <input-connects> section, or even replace that whole section with <input-connects/> if there are no other wanted inputs.

It seems to work - so far. Have I missed anything?