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I converted my Pluto to 40MHz reference input yesterday, taking care with a scope to check that the levels were correct (or at least the same as it was with the internal oscillator).
However, I was about 500Hz off frequency when receiving a test signal on 144MHz. It seems there is an offset stored in the Pluto relevant for the internal oscillator. I reset this with SDRC to 0ppm and it now works fine.