diff --git a/src/pygama/flow/data_loader.py b/src/pygama/flow/data_loader.py
index f1034c2f3..23810874f 100644
--- a/src/pygama/flow/data_loader.py
+++ b/src/pygama/flow/data_loader.py
@@ -1176,6 +1176,7 @@ def explode_evt_cols(el: pd.DataFrame, tier_table: Table):
                 table_length = len(f_entries)
 
                 log.debug(f"will load new columns {field_mask}")
+                # print(f"will load new columns {field_mask}")
 
                 # loop through each table in entry list and
                 # loop through each level we're asked to load from
@@ -1188,8 +1189,12 @@ def explode_evt_cols(el: pd.DataFrame, tier_table: Table):
                     # loop over tiers in the level
                     for tier in self.tiers[level]:
                         if tb not in col_tiers[file]["tables"][tier]:
+                            # print(f"Cannot find table {tb} in col_tiers tier {tier}")
                             continue
 
+                        # print(
+                        #    f"...for stream '{self.filedb.get_table_name(tier, tb)}' (at {level} level)"
+                        # )                        
                         log.debug(
                             f"...for stream '{self.filedb.get_table_name(tier, tb)}' (at {level} level)"
                         )
@@ -1584,10 +1589,12 @@ def get_tiers_for_col(
                     for tier in self.tiers[level]:
                         col_tiers[file]["tables"][tier] = []
                         tier_col_idx = self.filedb.df.loc[file, f"{tier}_col_idx"]
+                        # print(f"{tier}_col_idx: {tier_col_idx}")
                         if tier_col_idx is not None:
                             # Loop over tables
                             for i in range(len(tier_col_idx)):
                                 col_idx = self.filedb.df.loc[file, f"{tier}_col_idx"][i]
+                                # print(f"col_idx: {col_idx}")
                                 if col_idx in col_inds:
                                     col_tiers[file]["tables"][tier].append(
                                         self.filedb.df.loc[file, f"{tier}_tables"][i]
diff --git a/src/pygama/flow/file_db.py b/src/pygama/flow/file_db.py
index c64e6b786..4683737c0 100644
--- a/src/pygama/flow/file_db.py
+++ b/src/pygama/flow/file_db.py
@@ -149,6 +149,7 @@ def __init__(self, config: str | dict | list[str], scan: bool = True) -> None:
         names = list(np.unique(names))
         names += [f"{tier}_file" for tier in self.tiers]  # the generated file names
         names += [f"{tier}_size" for tier in self.tiers]  # file sizes
+
         names += ["file_status"]  # bonus columns
 
         self.df = pd.DataFrame(columns=names)
@@ -271,10 +272,13 @@ def scan_files(self, dirs: list[str] = None) -> None:
 
         # fill the main DataFrame
         self.df = pd.concat([self.df, temp_df])
-
+        
         # convert cols to numeric dtypes where possible
         for col in self.df.columns:
             self.df[col] = pd.to_numeric(self.df[col], errors="ignore")
+            
+        # Remove duplicates in the 'sortby' column 
+        self.df.drop_duplicates(subset=[self.sortby], inplace=True, ignore_index=True)
 
         # sort rows according to timestamps
         utils.inplace_sort(self.df, self.sortby)
@@ -358,16 +362,15 @@ def scan_tables_columns(
         """
         log.info("getting table column names")
 
-        if self.columns is not None:
-            if not override:
-                log.warning(
-                    "LH5 tables/columns names already set, if you want to perform the scan anyway, set override=True"
-                )
-                return
-            else:
-                log.warning("overwriting existing LH5 tables/columns names")
+        if override:
+            log.warning("overwriting existing LH5 tables/columns names")
 
         def update_tables_cols(row, tier: str, utc_cache: dict = None) -> pd.Series:
+            # Skip this row if it already has values and override is false
+            if set([f"{tier}_tables", f"{tier}_col_idx"]).issubset(self.df.columns):
+                if not override and not row[[f"{tier}_tables", f"{tier}_col_idx"]].isnull().any():
+                    return row[[f"{tier}_tables", f"{tier}_col_idx"]]
+            
             fpath = os.path.join(
                 self.data_dir,
                 self.tier_dirs[tier].lstrip("/"),
@@ -448,7 +451,10 @@ def update_tables_cols(row, tier: str, utc_cache: dict = None) -> pd.Series:
                 utc_cache[this_dir] = series
             return series
 
-        columns = []
+        if self.columns is None:
+            columns = []
+        else:
+            columns = self.columns
 
         # set up a cache to provide a fast option if all files in each directory
         # are expected to all have the same cols