If someone said don’t put your groceries in the engine compartment of your car… would you also assume the engine shouldn’t be there? 
What the docs are referring too is don’t put your main running code there, use the bare minimum needed in the void loop() stuff that needs to runs hundreds/thousands of times a second like Blynk.run() and timer.run() and perhaps even some simple connection checking routines, and use dedicated, timed, functions & loops for the rest of the code.
As for what is causing your disconnections… could literally be anything… bad code, bad power, bad WiFi, bad dog… we don’t know enough to even guess…