Update R handles in-place (#6903)

* update R handles in-place #fixes 6896

* update test to expect non-null handle

* remove unused variable

* fix failing tests

* solve linter complains

R-package/tests/testthat/test_model_compatibility.R

@@ -83,6 +83,7 @@ test_that("Models from previous versions of XGBoost can be loaded", {
       if (is_rds && compareVersion(model_xgb_ver, '1.1.1.1') < 0) {
         booster <- readRDS(model_file)
         expect_warning(predict(booster, newdata = pred_data))
+        booster <- readRDS(model_file)
         expect_warning(run_booster_check(booster, name))
       } else {
         if (is_rds) {