I just went through the VP2 console and ISS PDFs, searching both on setup and maintenance, and I can't find any reference to setup mode being useful during maintenance, especially of the rain gauge.
The ISS is a transmitter only, and knows nothing of what any receiving console or Envoy is doing. I believe, as noted in other threads here, the rain reading is sent as a serial number of tips since last reset, and that it rolls over at 255(?) This assures that all rain will be recorded by a console, even if a packet or 2 is lost. The console stops receiving ISS transmissions in setup mode, which would stop erroneous wind, temperature, and humidity from being recorded, but when put back in Current Weather Mode, it will receive and record whatever rain fall value the ISS is sending.
So, as labob has noted, the correct thing to do when cleaning or messing with the rain gauge is to unplug it from the SIM board before even taking off the rain cone.
Just put your console in setup mode, as described in the user manual.