diff --git a/src/core/base.py b/src/core/base.py
index e8c6de6..8a31e78 100644
--- a/src/core/base.py
+++ b/src/core/base.py
@@ -13,44 +13,17 @@ logger = logging.getLogger(__name__)
 class MigrationContext:
     """Holds state and connections for reading from Discord and writing to the target platform."""
     
-    def __init__(self, config: AppConfig, target_platform: str | None = None, source_mode: str = "live"):
+    def __init__(self, config: AppConfig, target_platform: str | None = None, source_mode: str = "live", base_dir: str = ""):
         self.config = config
         self.source_mode = source_mode
         # If caller didn't specify, fall back to config value
         self.target_platform = target_platform or config.target_platform or "fluxer"
-        
-        server_id = config.target_server_id or "unconfigured"
-        fillers = {"000000000000000000", "DISCORD_SERVER_ID", "FLUXER_COMMUNITY_ID",
-                   "STOAT_SERVER_ID", "TARGET_SERVER_ID", ""}
-        if server_id in fillers:
-            server_id = "unconfigured"
-        
-        # Try to find an existing state folder for this server_id
-        import os
-        
-        state_file: str | Path = ""
-        messages_file: str | Path = ""
-        
-        if server_id != "unconfigured":
-            logger.info(f"Probing for existing migration folder for Server ID: {server_id}")
-            for d in Path(".").iterdir():
-                if d.is_dir() and d.name.endswith(f"-{server_id}"):
-                    logger.info(f"Targeting existing folder: {d.name}")
-                    state_file = d / "state-migration.json"
-                    messages_file = d / "message-tracker.json"
-                    break
-            else:
-                logger.info(f"No existing folder found for {server_id}. A new one will be created upon first state change.")
-
-        self.state = MigrationState(
-            state_file=state_file,
-            messages_file=messages_file
-        )
+        self.state = MigrationState()
         
         # Select the appropriate source reader
         if source_mode == "backup":
             from src.core.backup_reader import BackupReader
-            backup_path = self._find_backup_path(config.discord_server_id)
+            backup_path = self._find_backup_path(config.discord_server_id, base_dir)
             self.discord_reader = BackupReader(backup_path)
             logger.info(f"Source mode: BACKUP — reading from {backup_path}")
         else:
@@ -76,16 +49,26 @@ class MigrationContext:
         
         self.is_running = False
 
-    @staticmethod
-    def _find_backup_path(server_id: str) -> Path:
+    def _find_backup_path(self, server_id: str, base_dir_str: str) -> Path:
         """Searches workspace for a DISCORD_BACKUP-{server_id} directory. Creates it if missing."""
+        base_dir = Path(base_dir_str) if base_dir_str else Path(".")
+        
+        # 1. Search inside the specific workspace directory first
+        if base_dir.exists() and base_dir.is_dir():
+            for d in base_dir.iterdir():
+                if d.is_dir() and d.name.endswith(f"-{server_id}") and "DISCORD_BACKUP" in d.name:
+                    logger.info(f"Found backup directory: {d}")
+                    return d
+                    
+        # 2. Fallback to global search if it wasn't found in the workspace
         for d in Path(".").rglob(f"DISCORD_BACKUP-{server_id}"):
             if d.is_dir():
-                logger.info(f"Found backup directory: {d}")
+                logger.info(f"Found backup directory globally: {d}")
                 return d
         
-        # If not found, create it in the current directory
-        new_path = Path(".") / f"DISCORD_BACKUP-{server_id}"
+        # If not found anywhere, create it inside the workspace
+        base_dir.mkdir(exist_ok=True)
+        new_path = base_dir / f"DISCORD_BACKUP-{server_id}"
         logger.info(f"No existing backup directory found for {server_id}. Creating new one: {new_path}")
         new_path.mkdir(exist_ok=True)
         return new_path
diff --git a/src/core/state.py b/src/core/state.py
index 26b1267..53a49e7 100644
--- a/src/core/state.py
+++ b/src/core/state.py
@@ -323,15 +323,21 @@ class MigrationState:
         new_folder = base / f"{clean_name}-{server_id}"
         logger.info(f"Setting active migration folder: {new_folder}")
         
-        # If we have an existing folder that is different, rename it
-        if self.state_file and self.state_file.parent.exists() and self.state_file.parent != new_folder:
-            # Check if it's actually in a server-specific folder (not roots)
-            if self.state_file.parent.name.endswith(f"-{server_id}"):
-                logger.info(f"Renaming active folder from {self.state_file.parent.name} to {new_folder.name}")
-                try:
-                    self.state_file.parent.rename(new_folder)
-                except Exception as e:
-                    logger.debug(f"Could not rename {self.state_file.parent} to {new_folder}: {e}")
+        # 1. Search base_dir to see if an older folder for this server_id exists
+        existing_folder: Path | None = None
+        if base.exists() and base.is_dir():
+            for d in base.iterdir():
+                if d.is_dir() and d.name.endswith(f"-{server_id}"):
+                    existing_folder = d
+                    break
+                    
+        # 2. Rename it if it doesn't match the new desired name
+        if existing_folder and existing_folder != new_folder:
+            logger.info(f"Renaming existing folder {existing_folder.name} to {new_folder.name}")
+            try:
+                existing_folder.rename(new_folder)
+            except Exception as e:
+                logger.debug(f"Could not rename {existing_folder} to {new_folder}: {e}")
 
         new_folder.mkdir(parents=True, exist_ok=True)
         
diff --git a/src/disco_reaper/exporter.py b/src/disco_reaper/exporter.py
index 490c8b3..bd9d91d 100644
--- a/src/disco_reaper/exporter.py
+++ b/src/disco_reaper/exporter.py
@@ -300,7 +300,7 @@ class DiscordExporter:
             
         return data
 
-    async def export_channel_messages(self, channel_id: int, progress_callback=None, force=False, accumulated_count=0):
+    async def export_channel_messages(self, channel_id: int, progress_callback=None, force=False, accumulated_count=0, after_id: int | None = None):
         """Fetches and saves message history for a channel, handling incremental sync. Returns the total messages processed."""
         channel = await self.reader.get_channel(channel_id)
         if not channel:
@@ -372,7 +372,9 @@ class DiscordExporter:
         last_id = None
         
         # Load existing messages for incremental sync (skip if force)
-        if not force and json_file.exists():
+        if after_id is not None:
+            last_id = after_id
+        elif not force and json_file.exists():
             try:
                 with open(json_file, "r", encoding="utf-8") as f:
                     old_data = json.load(f)
@@ -669,7 +671,7 @@ class DiscordExporter:
 
         return data
 
-    async def export_threads(self, channel_id: int, progress_callback=None, force=False, accumulated_count=0):
+    async def export_threads(self, channel_id: int, progress_callback=None, force=False, accumulated_count=0, after_id: int | None = None):
         """Exports active and archived threads for a channel. Returns accumulated message count."""
         channel = await self.reader.get_channel(channel_id)
         if not hasattr(channel, "threads") and not hasattr(channel, "public_archived_threads"):
@@ -711,7 +713,7 @@ class DiscordExporter:
             await asyncio.sleep(0) # important yield between threads
             
             # First backup the full thread — this creates {thread_id}.json with totalAttachmentSizeBytes
-            accumulated_count = await self.export_channel_messages(thread.id, progress_callback=progress_callback, force=force, accumulated_count=accumulated_count)
+            accumulated_count = await self.export_channel_messages(thread.id, progress_callback=progress_callback, force=force, accumulated_count=accumulated_count, after_id=after_id)
             thread_count += 1
 
             # Then populate the forum root JSON with the starter message
diff --git a/src/ui/backup_ops.py b/src/ui/backup_ops.py
index 3a56c1b..821e7c6 100644
--- a/src/ui/backup_ops.py
+++ b/src/ui/backup_ops.py
@@ -47,7 +47,7 @@ class BackupPane(Container):
         self.cfg_name = cfg_name
         self.config_path = cfg_path
         self.config = load_config(cfg_path)
-        self.engine = MigrationContext(self.config, target_platform=self.config.target_platform or "fluxer")
+        self.engine = MigrationContext(self.config, target_platform=self.config.target_platform or "fluxer", base_dir=f"Reaper-{self.cfg_name}")
         self.exporter = DiscordExporter(self.engine.discord_reader, base_dir=f"Reaper-{self.cfg_name}")
 
     def compose(self) -> ComposeResult:
@@ -74,7 +74,7 @@ class BackupPane(Container):
 
     def reload_config(self) -> None:
         self.config = load_config(self.config_path)
-        self.engine = MigrationContext(self.config, target_platform=self.config.target_platform or "fluxer")
+        self.engine = MigrationContext(self.config, target_platform=self.config.target_platform or "fluxer", base_dir=f"Reaper-{self.cfg_name}")
         self.exporter = DiscordExporter(self.engine.discord_reader, base_dir=f"Reaper-{self.cfg_name}")
         self._validate()
 
diff --git a/src/ui/shuttle_ops.py b/src/ui/shuttle_ops.py
index 346a9a2..14b9268 100644
--- a/src/ui/shuttle_ops.py
+++ b/src/ui/shuttle_ops.py
@@ -144,7 +144,7 @@ class ShuttlePane(Container):
 
     def _rebuild_engine(self):
         source = "backup" if self.config.tool_mode == "backup_transfer" else "live"
-        self.engine = MigrationContext(self.config, self.target_platform, source_mode=source)
+        self.engine = MigrationContext(self.config, self.target_platform, source_mode=source, base_dir=self._base_dir())
 
     # ── labels ────────────────────────────────────────────────────────────