Neither SBB, the Swiss rail system, nor Trenitalia, the Italian one, is showing this interruption in service on the schedules for that day. Last summer, I found that planned interruptions like this were apparent from the schedules months ahead (they affected our travels from Switzerland to Verona on the day we needed to travel). But maybe it just hasn’t be firmed up in the schedules yet.
If you are concerned, you have several alternatives.
One is to take the bus portion of the Bernina Express, from Tirano to Lugano, as well, then continue to Milan from Lugano.
The other would be to head from Zurich airport to Luzern, and take the Gotthard Panorama Express instead. This is a scenic journey by boat and train, down Vierwaldstättersee (Lake Lucerne) to Flüelen, boarding a train there for the scenic journey over the Gotthard pass route to Lugano.
https://www.sbb.ch/en/leisure-holidays/holidays-switzerland/panorama-trips/gotthard-panorama-express.html