You want to use updateSelectInput and then use observeEvent to catch when a filter value changes.
library(shiny)
library(shinydashboard) 
rm(list=ls())
#####/UI/####
header <- dashboardHeader()
sidebar <- dashboardSidebar()
body <- dashboardBody(
  selectInput(inputId = "filter1", label = "Filter 1", selected = "ALL",
              choices = c("ALL", "Bananas", "Apples", "Oranges")
  ),
  selectInput(inputId = "filter2", label = "Filter 2", selected = "ALL",
              choices = c("ALL", "Carrots", "Peas", "Celery")
  )
)
ui <- dashboardPage(header, sidebar, body)
#####/SERVER/####
server <- function(session, input, output) { 
  observeEvent(input$filter2,{
    if (input$filter2 != "ALL") {
      updateSelectInput(session, "filter1", selected = "ALL")
      }
  })
  observeEvent(input$filter1,{
    if (input$filter1 != "ALL") {
      updateSelectInput(session, "filter2", selected = "ALL")
    }
  })
  }
shinyApp(ui, server)