Checks for both flags

weed/shell/command_fs_configure.go

@@ -165,14 +165,22 @@ func infoAboutSimulationMode(writer io.Writer, forceMode bool, forceModeOption s
 // value to the new flag. This ensures that explicit -force=false takes precedence.
 func handleDeprecatedForceFlag(writer io.Writer, fs *flag.FlagSet, forceAlias *bool, applyFlag *bool) {
 	forceIsSet := false
+	applyIsSet := false
 	fs.Visit(func(f *flag.Flag) {
-		if f.Name == "force" {
+		switch f.Name {
+		case "force":
 			forceIsSet = true
+		case "apply":
+			applyIsSet = true
 		}
 	})
 
 	if forceIsSet {
-		fmt.Fprintf(writer, "WARNING: -force is deprecated, please use -apply instead\n")
+		if applyIsSet {
+			fmt.Fprintf(writer, "WARNING: both -force and -apply are set. -force is deprecated and takes precedence. Please use only -apply.\n")
+		} else {
+			fmt.Fprintf(writer, "WARNING: -force is deprecated, please use -apply instead.\n")
+		}
 		*applyFlag = *forceAlias
 	}
 }