Thank you for posting here. If the waveguide elements are not in feedback loops, then the delay compensation usually is not critical, but still good to have. The total number of delay compensation should add up to the total number of connections in the loop. It is hard to say what's the problem without the file, but I'd recommend testing the external feedback link with an Optical Network Analyzer using the "impulse response" in time domain to make sure it mataches the result in frequency domain. Please give this a try and let me know what you find.
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