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Tough question. There are no easy answers using the methods that you currently apply. A parallel network for the monitoring is one option – but probably not what you want to hear.
If you supplement your monitoring with active probing measurement methodologies, you may be able to avoid the effect of the maintenance and monitoring. Active probing/sampling provides real-time measures of your network. If you could arrange measurements of your real-time performance when you know monitoring/maintenance is not occurring along a particular path, you can measure instantaneous utilization. And even if you can't, statistically you are not likely to see any particular utilization and would typically get representative views of your network performance.
Some sampling methods are non-intrusive and can be used without adding utilization.
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