Found a fix, maybe for the saving issues. Checked out some other forks of worldborder, and noticed that this seemed to help @Brokkonaut -> Author who fixed the issue.

src/main/java/com/wimbli/WorldBorder/Config.java

@@ -420,9 +420,9 @@ public class Config {
             logConfig("Border-checking timed task stopped.");
     }
 
-    public static void StopFillTask() {
+    public static void StopFillTask(boolean Save) {
         if (fillTask != null && fillTask.valid())
-            fillTask.cancel();
+            fillTask.cancel(Save);
     }
 
     public static void StoreFillTask() {
@@ -589,16 +589,15 @@ public class Config {
         ConfigurationSection storedFillTask = cfg.getConfigurationSection("fillTask");
         if (storedFillTask != null) {
             String worldName = storedFillTask.getString("world");
-            int fillDistance = storedFillTask.getInt("fillDistance", 176);
-            int chunksPerRun = storedFillTask.getInt("chunksPerRun", 5);
-            int tickFrequency = storedFillTask.getInt("tickFrequency", 20);
+            int fillDistance = storedFillTask.getInt("fillDistance", 208);
+            int chunksPerRun = storedFillTask.getInt("chunksPerRun", 2);
+            int tickFrequency = storedFillTask.getInt("tickFrequency", 5);
             int fillX = storedFillTask.getInt("x", 0);
             int fillZ = storedFillTask.getInt("z", 0);
             int fillLength = storedFillTask.getInt("length", 0);
             int fillTotal = storedFillTask.getInt("total", 0);
             boolean forceLoad = storedFillTask.getBoolean("forceLoad", false);
             RestoreFillTask(worldName, fillDistance, chunksPerRun, tickFrequency, fillX, fillZ, fillLength, fillTotal, forceLoad);
-            save(false);
         }
 
         if (logIt)

src/main/java/com/wimbli/WorldBorder/WorldBorder.java

@@ -45,7 +45,7 @@ public class WorldBorder extends JavaPlugin {
         DynMapFeatures.removeAllBorders();
         Config.StopBorderTimer();
         Config.StoreFillTask();
-        Config.StopFillTask();
+        Config.StopFillTask(true);
     }
 
     // for other plugins to hook into

src/main/java/com/wimbli/WorldBorder/WorldFillTask.java

@@ -78,21 +78,21 @@ public class WorldFillTask implements Runnable {
                 sendMessage("You must specify a world!");
             else
                 sendMessage("World \"" + worldName + "\" not found!");
-            this.stop();
+            this.stop(true);
             return;
         }
 
         this.border = (Config.Border(worldName) == null) ? null : Config.Border(worldName).copy();
         if (this.border == null) {
             sendMessage("No border found for world \"" + worldName + "\"!");
-            this.stop();
+            this.stop(false);
             return;
         }
 
         // load up a new WorldFileData for the world in question, used to scan region files for which chunks are already fully generated and such
         worldData = WorldFileData.create(world, notifyPlayer);
         if (worldData == null) {
-            this.stop();
+            this.stop(false);
             return;
         }
 
@@ -123,7 +123,7 @@ public class WorldFillTask implements Runnable {
     }
 
     public void setTaskID(int ID) {
-        if (ID == -1) this.stop();
+        if (ID == -1) this.stop(false);
         this.taskID = ID;
     }
 
@@ -226,7 +226,7 @@ public class WorldFillTask implements Runnable {
 
             // if this iteration has been running for 45ms (almost 1 tick) or more, stop to take a breather
             if (now > loopStartTime + 45) {
-                System.out.println("PAUSED FOR DEBUG");
+                //System.out.println("PAUSED FOR DEBUG");
                 readyToGo = true;
                 return;
             }
@@ -350,16 +350,17 @@ public class WorldFillTask implements Runnable {
         world.save();
         Bukkit.getServer().getPluginManager().callEvent(new WorldBorderFillFinishedEvent(world, reportTotal));
         sendMessage("task successfully completed for world \"" + refWorld() + "\"!");
-        this.stop();
+        this.stop(false);
     }
 
     // for cancelling prematurely
-    public void cancel() {
-        this.stop();
+    public void cancel(boolean Save) {
+        this.stop(Save);
     }
 
     // we're done, whether finished or cancelled
-    private void stop() {
+    private void stop(boolean Save) {
+        if (!Save) Config.UnStoreFillTask();
         if (server == null)
             return;
 
@@ -403,8 +404,7 @@ public class WorldFillTask implements Runnable {
         if (this.paused) {
             Config.StoreFillTask();
             reportProgress();
-        } else
-            Config.UnStoreFillTask();
+        }
     }
 
     public boolean isPaused() {
@@ -439,6 +439,7 @@ public class WorldFillTask implements Runnable {
             lastAutosave = lastReport;
             sendMessage("Saving the world to disk, just to be on the safe side.");
             world.save();
+            Config.StoreFillTask();
         }
     }
 
@@ -471,6 +472,10 @@ public class WorldFillTask implements Runnable {
         this.length = length;
         this.reportTotal = totalDone;
         this.continueNotice = true;
+        this.refX = x;
+        this.refZ = z;
+        this.refLength = length;
+        this.refTotal = totalDone;
     }
 
     public int refX() {

src/main/java/com/wimbli/WorldBorder/cmd/CmdFill.java

@@ -48,7 +48,7 @@ public class CmdFill extends WBCmd {
                     return;
                 sender.sendMessage(C_HEAD + "Cancelling the world map generation task.");
                 fillDefaults();
-                Config.StopFillTask();
+                Config.StopFillTask(true);
                 return;
             } else if (check.equals("pause")) {
                 if (!makeSureFillIsRunning(sender))

src/main/resources/plugin.yml

@@ -2,7 +2,7 @@ name: WorldBorder
 authors: [Brettflan, PryPurity]
 description: Efficient, feature-rich plugin for limiting the size of your worlds.
 version: 2.0.8
-api-version: 1.16
+api-version: 1.15
 main: com.wimbli.WorldBorder.WorldBorder
 softdepend:
   - dynmap