R leaflet - Show/Hide addControl() element with group layers

Alright, now I think i understand your problem. Below is another example, which shows only the legend and control of the active groups. For that, I created 2 html_legends for group A and for group B.

library(shiny)
library(leaflet)

html_legend_A <- "<img src='http://leafletjs.com/docs/images/leaf-green.png'>green<br/>"
html_legend_B <- "<img src='http://leafletjs.com/docs/images/leaf-red.png'>red<br/>"

ui <- fluidPage(
  leafletOutput("map")
)
server <- function(input, output, session){
  output$map <- renderLeaflet({
    map <- leaflet(data = quakes) %>% addTiles() %>%
      addMarkers(~long, ~lat, icon = leafIcons, group = "Group A", layerId = "A") %>%
      addMarkers(~long, ~lat, icon = leafIcons, group = "Group B", layerId = "B") %>%
      addLayersControl(position = "topleft", overlayGroups = c("Group A","Group B"))
    map
  })

  observe({
    map <- leafletProxy("map") %>% clearControls()
    if (any(input$map_groups %in% "Group A")) {
      map <- map %>% 
        addControl(html = html_legend_A, layerId = "A", position = "bottomleft") %>% 
        addLegend(title="Group A", position="bottomright", opacity=1, colors="green",labels = "Group A")}
    if (any(input$map_groups %in% "Group B")) {
      map <- map %>% 
        addControl(html = html_legend_B, layerId = "B", position = "bottomleft") %>% 
        addLegend(title="Group B", position="bottomright", opacity=1,colors="red",labels = "Group B")}
  })
}

shinyApp(ui, server)

When using the LayerId argument, it only shows 1 marker per group. If you want to see all markers, the LayerId argument should not be given. I made you another example. I think this should be right now :) I also create 2 icons and I am filtering the quakes data, based on the mag-column inside the renderLeaflet function, as you do in the icon assignment.

library(shiny)
library(leaflet)

data(quakes)
quakes <- quakes[1:10,]

leafIcons_A <- icons(
  iconUrl = "https://leafletjs.com/examples/custom-icons/leaf-green.png",
  iconWidth = 38, iconHeight = 95,
  iconAnchorX = 22, iconAnchorY = 94)
leafIcons_B <- icons(
  iconUrl = "https://leafletjs.com/examples/custom-icons/leaf-red.png",
  iconWidth = 38, iconHeight = 95,
  iconAnchorX = 22, iconAnchorY = 94)

html_legend_A <- "<img src='https://leafletjs.com/examples/custom-icons/leaf-green.png'>green<br/>"
html_legend_B <- "<img src='https://leafletjs.com/examples/custom-icons/leaf-red.png'>red<br/>"

ui <- fluidPage(
  leafletOutput("map")
)
server <- function(input, output, session){
  output$map <- renderLeaflet({
    dataA <- quakes[quakes$mag < 4.6,]
    dataB <- quakes[quakes$mag > 4.6,]

    map <- leaflet() %>% addTiles() %>%
      addMarkers(dataA$long, dataA$lat, icon = leafIcons_A, group = "Group A") %>%
      addMarkers(dataB$long, dataB$lat, icon = leafIcons_B, group = "Group B") %>%
      addLayersControl(position = "topleft", overlayGroups = c("Group A","Group B"))
    map
  })

  observe({
    map <- leafletProxy("map") %>% clearControls()
    if (any(input$map_groups %in% "Group A")) {
      map <- map %>%
        addControl(html = html_legend_A, position = "bottomleft") %>%
        addLegend(title="Group A", position="bottomright", opacity=1, colors="green",labels = "Group A")}
    if (any(input$map_groups %in% "Group B")) {
      map <- map %>%
        addControl(html = html_legend_B, position = "bottomleft") %>%
        addLegend(title="Group B", position="bottomright", opacity=1,colors="red",labels = "Group B")}
  })
}

shinyApp(ui, server)